diff --git a/examples/offline_inference/qwen3_omni/only_thinker.py b/examples/offline_inference/qwen3_omni/only_thinker.py
new file mode 100644
index 0000000000000..88a61ed694c2e
--- /dev/null
+++ b/examples/offline_inference/qwen3_omni/only_thinker.py
@@ -0,0 +1,170 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright contributors to the vLLM project
+"""
+This example shows how to use vLLM for running offline inference
+with the correct prompt format on Qwen2.5-Omni (thinker only).
+"""
+
+from typing import NamedTuple
+
+from vllm import LLM, SamplingParams
+from vllm.assets.audio import AudioAsset
+from vllm.assets.image import ImageAsset
+from vllm.assets.video import VideoAsset
+from vllm.multimodal.image import convert_image_mode
+from vllm.utils.argparse_utils import FlexibleArgumentParser
+
+
+class QueryResult(NamedTuple):
+    inputs: dict
+    limit_mm_per_prompt: dict[str, int]
+
+
+# NOTE: The default `max_num_seqs` and `max_model_len` may result in OOM on
+# lower-end GPUs.
+# Unless specified, these settings have been tested to work on a single L4.
+
+default_system = (
+    "You are Qwen, a virtual human developed by the Qwen Team, Alibaba "
+    "Group, capable of perceiving auditory and visual inputs, as well as "
+    "generating text and speech."
+)
+
+
+def get_mixed_modalities_query() -> QueryResult:
+    question = (
+        "What is recited in the audio? "
+        "What is the content of this image? Why is this video funny?"
+    )
+    prompt = (
+        f"<|im_start|>system\n{default_system}<|im_end|>\n"
+        "<|im_start|>user\n<|audio_start|><|audio_pad|><|audio_end|>"
+        "<|vision_start|><|image_pad|><|vision_end|>"
+        "<|vision_start|><|video_pad|><|vision_end|>"
+        f"{question}<|im_end|>\n"
+        f"<|im_start|>assistant\n"
+    )
+    return QueryResult(
+        inputs={
+            "prompt": prompt,
+            "multi_modal_data": {
+                "audio": AudioAsset("mary_had_lamb").audio_and_sample_rate,
+                "image": convert_image_mode(
+                    ImageAsset("cherry_blossom").pil_image, "RGB"
+                ),
+                "video": VideoAsset(name="baby_reading", num_frames=16).np_ndarrays,
+            },
+        },
+        limit_mm_per_prompt={"audio": 1, "image": 1, "video": 1},
+    )
+
+
+def get_use_audio_in_video_query() -> QueryResult:
+    question = (
+        "Describe the content of the video in details, then convert what the "
+        "baby say into text."
+    )
+    prompt = (
+        f"<|im_start|>system\n{default_system}<|im_end|>\n"
+        "<|im_start|>user\n<|vision_start|><|video_pad|><|vision_end|>"
+        f"{question}<|im_end|>\n"
+        f"<|im_start|>assistant\n"
+    )
+    asset = VideoAsset(name="baby_reading", num_frames=16)
+    audio = asset.get_audio(sampling_rate=16000)
+    return QueryResult(
+        inputs={
+            "prompt": prompt,
+            "multi_modal_data": {
+                "video": asset.np_ndarrays,
+                "audio": audio,
+            },
+            "mm_processor_kwargs": {
+                "use_audio_in_video": True,
+            },
+        },
+        limit_mm_per_prompt={"audio": 1, "video": 1},
+    )
+
+
+def get_multi_audios_query() -> QueryResult:
+    question = "Are these two audio clips the same?"
+    prompt = (
+        f"<|im_start|>system\n{default_system}<|im_end|>\n"
+        "<|im_start|>user\n<|audio_start|><|audio_pad|><|audio_end|>"
+        "<|audio_start|><|audio_pad|><|audio_end|>"
+        f"{question}<|im_end|>\n"
+        f"<|im_start|>assistant\n"
+    )
+    return QueryResult(
+        inputs={
+            "prompt": prompt,
+            "multi_modal_data": {
+                "audio": [
+                    AudioAsset("winning_call").audio_and_sample_rate,
+                    AudioAsset("mary_had_lamb").audio_and_sample_rate,
+                ],
+            },
+        },
+        limit_mm_per_prompt={
+            "audio": 2,
+        },
+    )
+
+
+query_map = {
+    "mixed_modalities": get_mixed_modalities_query,
+    "use_audio_in_video": get_use_audio_in_video_query,
+    "multi_audios": get_multi_audios_query,
+}
+
+
+def main(args):
+    model_name = "Qwen/Qwen3-Omni-30B-A3B-Instruct"
+    query_result = query_map[args.query_type]()
+
+    llm = LLM(
+        model=model_name,
+        max_model_len=12800,
+        max_num_seqs=5,
+        limit_mm_per_prompt=query_result.limit_mm_per_prompt,
+        seed=args.seed,
+    )
+
+    # We set temperature to 0.2 so that outputs can be different
+    # even when all prompts are identical when running batch inference.
+    sampling_params = SamplingParams(temperature=0.2, max_tokens=256)
+
+    outputs = llm.generate(query_result.inputs, sampling_params=sampling_params)
+
+    for o in outputs:
+        generated_text = o.outputs[0].text
+        print(generated_text)
+
+
+def parse_args():
+    parser = FlexibleArgumentParser(
+        description="Demo on using vLLM for offline inference with "
+        "audio language models"
+    )
+    parser.add_argument(
+        "--query-type",
+        "-q",
+        type=str,
+        default="mixed_modalities",
+        choices=query_map.keys(),
+        help="Query type.",
+    )
+    parser.add_argument(
+        "--seed",
+        type=int,
+        default=None,
+        help="Set the seed when initializing `vllm.LLM`.",
+    )
+
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    args = parse_args()
+    main(args)
diff --git a/tests/model_executor/test_qwen3_omni.py b/tests/model_executor/test_qwen3_omni.py
new file mode 100644
index 0000000000000..c92c61dcd3bc2
--- /dev/null
+++ b/tests/model_executor/test_qwen3_omni.py
@@ -0,0 +1,221 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright contributors to the vLLM project
+
+from unittest.mock import Mock
+
+import pytest
+from transformers import PretrainedConfig
+
+from vllm.multimodal.processing import InputProcessingContext
+
+
+# Helper function to print input IDs with coalesced audio/video tokens.
+def print_input_ids(input_ids):
+    """
+    Print input IDs, compressing consecutive special tokens.
+    - 151675: <|audio_pad|>
+    - 151656: <|video_pad|>
+    """
+    if not input_ids:
+        print("[]")
+        return
+
+    result = []
+    i = 0
+
+    while i < len(input_ids):
+        current_id = input_ids[i]
+
+        # Check if it's a special token that should be compressed
+        if current_id in [151675, 151656]:
+            # Count consecutive occurrences
+            count = 1
+            while i + count < len(input_ids) and input_ids[i + count] == current_id:
+                count += 1
+
+            # Add compressed representation
+            token_name = "<|audio_pad|>" if current_id == 151675 else "<|video_pad|>"
+            result.append(f"{token_name} * {count}")
+            i += count
+        else:
+            # Regular token, just add it
+            result.append(str(current_id))
+            i += 1
+
+    print(", ".join(result))
+
+
+@pytest.fixture
+def mock_qwen3_omni_config():
+    """Create a mock Qwen3OmniMoeThinker config."""
+    config = Mock(spec=PretrainedConfig)
+    # Token IDs from https://huggingface.co/Qwen/Qwen3-Omni-30B-A3B-Instruct/blob/main/tokenizer_config.json
+    config.audio_token_id = 151675  # <|audio_pad|>
+    config.video_token_id = 151656  # <|video_pad|>
+    config.image_token_id = 151655  # <|image_pad|>
+    config.audio_start_token_id = 151669  # <|audio_start|>
+    config.audio_end_token_id = 151670  # <|audio_end|>
+    config.vision_start_token_id = 151652  # <|vision_start|>
+    config.position_id_per_seconds = 12.5
+
+    # Vision config
+    vision_config = Mock()
+    vision_config.spatial_merge_size = 2
+    config.vision_config = vision_config
+
+    return config
+
+
+@pytest.fixture
+def mock_processor():
+    """Create a mock HF processor."""
+    from transformers.models.whisper import WhisperFeatureExtractor
+
+    processor = Mock()
+    processor.audio_token = "<|audio_pad|>"
+    processor.image_token = "<|image_pad|>"
+    processor.video_token = "<|video_pad|>"
+
+    # Create a real WhisperFeatureExtractor instance for the feature_extractor attribute
+    feature_extractor = WhisperFeatureExtractor()
+    processor.feature_extractor = feature_extractor
+
+    return processor
+
+
+@pytest.fixture
+def mock_tokenizer():
+    """Create a mock tokenizer."""
+    tokenizer = Mock()
+    # Token IDs from https://huggingface.co/Qwen/Qwen3-Omni-30B-A3B-Instruct/blob/main/tokenizer_config.json
+    tokenizer.get_vocab = Mock(
+        return_value={
+            "<|audio_pad|>": 151675,
+            "<|video_pad|>": 151656,
+            "<|image_pad|>": 151655,
+            "<|audio_start|>": 151669,
+            "<|audio_end|>": 151670,
+            "<|vision_start|>": 151652,
+            "<|vision_end|>": 151653,
+        }
+    )
+    tokenizer.encode = Mock(
+        side_effect=lambda x: {
+            "<|vision_start|>": [151652],
+            "<|vision_end|>": [151653],
+            "<|audio_start|>": [151669],
+            "<|audio_end|>": [151670],
+            "<|audio_pad|>": [151675],
+            "<|image_pad|>": [151655],
+            "<|video_pad|>": [151656],
+        }.get(x, [0])
+    )
+    tokenizer.vision_bos_token = "<|vision_start|>"
+    tokenizer.vision_eos_token = "<|vision_end|>"
+    tokenizer.audio_bos_token = "<|audio_start|>"
+    tokenizer.audio_eos_token = "<|audio_end|>"
+    return tokenizer
+
+
+@pytest.fixture
+def mock_image_processor():
+    """Create a mock image processor."""
+    image_processor = Mock()
+    image_processor.merge_size = 2
+    return image_processor
+
+
+def test_qwen3_omni_get_updates_use_audio_in_video(
+    mock_qwen3_omni_config,
+    mock_processor,
+    mock_tokenizer,
+    mock_image_processor,
+):
+    """Test the get_updates_use_audio_in_video method directly."""
+
+    from vllm.model_executor.models.qwen3_omni_moe_thinker import (
+        Qwen3OmniMoeThinkerMultiModalProcessor,
+        Qwen3OmniMoeThinkerProcessingInfo,
+    )
+
+    # Create a mock context
+    mock_ctx = Mock(spec=InputProcessingContext)
+
+    # Create processing info
+    info = Qwen3OmniMoeThinkerProcessingInfo(mock_ctx)
+    info.get_hf_config = Mock(return_value=mock_qwen3_omni_config)
+    info.get_hf_processor = Mock(return_value=mock_processor)
+    info.get_tokenizer = Mock(return_value=mock_tokenizer)
+    info.get_image_processor = Mock(return_value=mock_image_processor)
+
+    # Create a mock dummy_inputs builder
+    mock_dummy_inputs = Mock()
+
+    # Create the processor
+    processor = Qwen3OmniMoeThinkerMultiModalProcessor(info, mock_dummy_inputs)
+
+    # Test parameters from reference video
+    # https://qianwen-res.oss-cn-beijing.aliyuncs.com/Qwen3-Omni/demo/draw.mp4
+    audio_len = 85
+    video_grid_thw = [6, 36, 64]
+    video_second_per_grid_t = 2.0
+
+    # Call the method
+    updates = processor.get_updates_use_audio_in_video(
+        thinker_config=mock_qwen3_omni_config,
+        audio_len=audio_len,
+        video_grid_thw=video_grid_thw,
+        video_second_per_grid_t=video_second_per_grid_t,
+    )
+
+    # Updated input ids should align with HF implementation.
+    # 151669,
+    # <|video_pad|> * 576, <|audio_pad|> * 25,
+    # <|video_pad|> * 576, <|audio_pad|> * 25,
+    # <|video_pad|> * 576, <|audio_pad|> * 25,
+    # <|video_pad|> * 576, <|audio_pad|> * 10,
+    # <|video_pad|> * 1152,
+    # 151670
+    print_input_ids(updates)
+
+    # Verify structure
+    assert isinstance(updates, list)
+    assert len(updates) > 0
+
+    # Verify start and end tokens
+    audio_start_token_id = mock_qwen3_omni_config.audio_start_token_id
+    audio_end_token_id = mock_qwen3_omni_config.audio_end_token_id
+
+    assert updates[0] == audio_start_token_id
+    assert updates[-1] == audio_end_token_id
+
+    # Verify both audio and video tokens are present
+    audio_token_id = mock_qwen3_omni_config.audio_token_id
+    video_token_id = mock_qwen3_omni_config.video_token_id
+
+    audio_count = updates.count(audio_token_id)
+    video_count = updates.count(video_token_id)
+
+    assert audio_count == audio_len, (
+        f"Expected {audio_len} audio tokens, got {audio_count}"
+    )
+
+    # Calculate expected video token count
+    spatial_merge_size = mock_qwen3_omni_config.vision_config.spatial_merge_size
+    height = video_grid_thw[1] // spatial_merge_size
+    width = video_grid_thw[2] // spatial_merge_size
+    expected_video_count = video_grid_thw[0] * height * width
+
+    assert video_count == expected_video_count, (
+        f"Expected {expected_video_count} video tokens, got {video_count}"
+    )
+
+    # Total tokens should be: 1 (start) + audio_len + video_count + 1 (end)
+    expected_total = 1 + audio_len + expected_video_count + 1
+    assert len(updates) == expected_total, (
+        f"Expected {expected_total} total tokens, got {len(updates)}"
+    )
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-v"])
diff --git a/vllm/model_executor/models/qwen2_5_omni_thinker.py b/vllm/model_executor/models/qwen2_5_omni_thinker.py
index 262ea771d9cdf..7506ee8656fda 100644
--- a/vllm/model_executor/models/qwen2_5_omni_thinker.py
+++ b/vllm/model_executor/models/qwen2_5_omni_thinker.py
@@ -23,7 +23,6 @@
 """Inference-only Qwen2.5-Omni model (thinker part)."""
 
 from collections.abc import Callable, Iterable, Mapping, Sequence
-from copy import copy
 from functools import partial
 from typing import Annotated, Any, Literal
 
@@ -387,15 +386,6 @@ class Qwen2_5OmniThinkerMultiModalProcessor(
         self._validate_mm_kwargs(mm_kwargs, mm_item_counts)
         self._validate_mm_updates(mm_prompt_updates, mm_item_counts)
 
-        use_audio_in_video = False
-        if "video" in mm_kwargs:
-            video_items = [item for item in mm_kwargs["video"] if item is not None]
-            # only check video items (if there are any)
-            if video_items:
-                use_audio_in_video = all(
-                    item["use_audio_in_video"].data for item in video_items
-                )
-
         if is_update_applied:
             mm_placeholders = self._find_mm_placeholders(
                 prompt_ids,
@@ -404,7 +394,6 @@ class Qwen2_5OmniThinkerMultiModalProcessor(
             self._validate_mm_placeholders(
                 mm_placeholders,
                 mm_item_counts,
-                use_audio_in_video=use_audio_in_video,
             )
         else:
             prompt_ids, mm_placeholders = self._apply_prompt_updates(
@@ -414,7 +403,6 @@ class Qwen2_5OmniThinkerMultiModalProcessor(
             self._validate_mm_placeholders(
                 mm_placeholders,
                 mm_item_counts,
-                use_audio_in_video=use_audio_in_video,
             )
 
         return prompt_ids, mm_placeholders
@@ -640,19 +628,6 @@ class Qwen2_5OmniThinkerMultiModalProcessor(
 
         return mm_processed_data
 
-    def _validate_mm_placeholders(
-        self,
-        mm_placeholders: Mapping[str, list[PlaceholderFeaturesInfo]],
-        mm_item_counts: Mapping[str, int],
-        use_audio_in_video: bool = False,
-    ) -> None:
-        if use_audio_in_video:
-            mm_item_counts = copy(mm_item_counts)
-            if "video" in mm_item_counts:
-                assert "audio" in mm_item_counts
-                mm_item_counts["audio"] -= mm_item_counts["video"]
-        super()._validate_mm_placeholders(mm_placeholders, mm_item_counts)
-
 
 class Qwen2_5OmniConditionalGenerationMixin:
     def _parse_and_validate_audio_input(
diff --git a/vllm/model_executor/models/qwen3_omni_moe_thinker.py b/vllm/model_executor/models/qwen3_omni_moe_thinker.py
index 61f218f16d79c..f5f88f66eff91 100755
--- a/vllm/model_executor/models/qwen3_omni_moe_thinker.py
+++ b/vllm/model_executor/models/qwen3_omni_moe_thinker.py
@@ -68,11 +68,11 @@ from vllm.multimodal import MULTIMODAL_REGISTRY
 from vllm.multimodal.inputs import MultiModalFeatureSpec, MultiModalKwargsItems
 from vllm.multimodal.parse import AudioProcessorItems, MultiModalDataItems
 from vllm.multimodal.processing import (
-    BaseMultiModalProcessor,
     MultiModalPromptUpdates,
     PlaceholderFeaturesInfo,
     PromptReplacement,
     PromptUpdate,
+    PromptUpdateDetails,
 )
 from vllm.sequence import IntermediateTensors
 
@@ -87,7 +87,6 @@ from .qwen2_5_omni_thinker import (
     Qwen2_5OmniConditionalGenerationMixin,
     Qwen2_5OmniThinkerDummyInputsBuilder,
     Qwen2_5OmniThinkerMultiModalProcessor,
-    Qwen2_5OmniThinkerProcessingInfo,
 )
 from .qwen2_5_vl import (
     Qwen2_5_VisionAttention,
@@ -807,24 +806,8 @@ class Qwen3OmniMoeThinkerMultiModalProcessor(
                 else:
                     use_audio_in_video = False
 
-        if use_audio_in_video and "video" in mm_item_counts:
-            assert "audio" in mm_item_counts
-            mm_item_counts["audio"] -= mm_item_counts["video"]
-
-        # Special case with `use_audio_in_video=True`
-        if use_audio_in_video:
-            if is_update_applied:
-                prompt_ids = self._get_raw_input_ids(prompt_ids, use_audio_in_video)
-            (
-                prompt_ids,
-                mm_placeholders,
-            ) = self._apply_prompt_updates(
-                prompt_ids,
-                mm_prompt_updates,
-            )
-            self._validate_mm_placeholders(mm_placeholders, mm_item_counts)
         # normal case with `use_audio_in_video=False`
-        elif is_update_applied:
+        if is_update_applied:
             mm_placeholders = self._find_mm_placeholders(
                 prompt_ids,
                 mm_prompt_updates,
@@ -834,10 +817,24 @@ class Qwen3OmniMoeThinkerMultiModalProcessor(
                 mm_item_counts,
             )
         else:
-            prompt_ids, mm_placeholders = self._apply_prompt_updates(
-                prompt_ids,
-                mm_prompt_updates,
-            )
+            if use_audio_in_video and "audio" in mm_prompt_updates:
+                filtered_updates = {
+                    k: v for k, v in mm_prompt_updates.items() if k != "audio"
+                }
+                prompt_ids, mm_placeholders = self._apply_prompt_updates(
+                    prompt_ids,
+                    filtered_updates,
+                )
+                # Derive audio placeholders from video placeholders
+                mm_placeholders = self._derive_audio_from_video_placeholders(
+                    mm_placeholders, mm_prompt_updates
+                )
+            else:
+                prompt_ids, mm_placeholders = self._apply_prompt_updates(
+                    prompt_ids,
+                    mm_prompt_updates,
+                )
+
             self._validate_mm_placeholders(
                 mm_placeholders,
                 mm_item_counts,
@@ -962,7 +959,9 @@ class Qwen3OmniMoeThinkerMultiModalProcessor(
 
         def get_replacement_qwen2_use_audio_in_video(item_idx: int):
             nonlocal audio_in_video_item_idx
-            audio_num_features = audio_output_lengths[audio_item_idx + item_idx]
+            audio_num_features = audio_output_lengths[
+                audio_in_video_item_idx + item_idx
+            ]
             video_grid_thw = out_mm_data["video_grid_thw"][item_idx]
 
             audio_in_video_item_idx += 1
@@ -971,14 +970,17 @@ class Qwen3OmniMoeThinkerMultiModalProcessor(
             if second_per_grid_ts:
                 video_second_per_grid_t = second_per_grid_ts[item_idx]
             else:
-                video_second_per_grid_t = 1.0
+                video_second_per_grid_t = 2.0
 
-            return self.get_updates_use_audio_in_video(
+            placeholder = self.get_updates_use_audio_in_video(
                 thinker_config=thinker_config,
                 audio_len=audio_num_features,
                 video_grid_thw=video_grid_thw,
                 video_second_per_grid_t=video_second_per_grid_t,
             )
+            return PromptUpdateDetails.select_token_id(
+                placeholder, embed_token_id=video_token_id
+            )
 
         video_replacement_fn = (
             get_replacement_qwen2_use_audio_in_video
@@ -1004,14 +1006,50 @@ class Qwen3OmniMoeThinkerMultiModalProcessor(
             ),
         ]
 
-    def _validate_mm_placeholders(
+    def _derive_audio_from_video_placeholders(
         self,
-        mm_placeholders: Mapping[str, list[PlaceholderFeaturesInfo]],
-        mm_item_counts: Mapping[str, int],
-    ) -> None:
-        BaseMultiModalProcessor[
-            Qwen2_5OmniThinkerProcessingInfo
-        ]._validate_mm_placeholders(self, mm_placeholders, mm_item_counts)
+        placeholders: Mapping[str, list[PlaceholderFeaturesInfo]],
+        mm_prompt_updates: MultiModalPromptUpdates,
+    ) -> Mapping[str, list[PlaceholderFeaturesInfo]]:
+        """
+        Helper to derive audio placeholders from video placeholders when
+        use_audio_in_video=True.
+        """
+        if "video" not in placeholders:
+            return placeholders
+
+        # Validate audio and video counts match
+        num_videos = len(placeholders["video"])
+        num_audios = len(mm_prompt_updates.get("audio", []))
+        if num_audios != num_videos:
+            raise ValueError(
+                f"use_audio_in_video requires equal number of audio and video items, "
+                f"got {num_audios=}, {num_videos=}"
+            )
+
+        tokenizer = self.info.get_tokenizer()
+        processor = self.info.get_hf_processor()
+        audio_token_id = tokenizer.get_vocab()[processor.audio_token]
+
+        result_placeholders = dict(placeholders)
+        audio_placeholders = []
+
+        # Each video is paired with one audio
+        for video_idx, video_placeholder in enumerate(placeholders["video"]):
+            # Create is_embed mask selecting only audio tokens
+            audio_is_embed = torch.tensor(video_placeholder.tokens) == audio_token_id
+
+            audio_placeholder = PlaceholderFeaturesInfo(
+                modality="audio",
+                item_idx=video_idx,
+                start_idx=video_placeholder.start_idx,
+                tokens=video_placeholder.tokens,
+                is_embed=audio_is_embed,
+            )
+            audio_placeholders.append(audio_placeholder)
+
+        result_placeholders["audio"] = audio_placeholders
+        return result_placeholders
 
     def _get_raw_input_ids(
         self,
@@ -1454,7 +1492,11 @@ class Qwen3OmniMoeThinkerForConditionalGeneration(
             )
 
         if not len(second_per_grid_ts) and len(video_grid_thw):
-            second_per_grids = torch.ones(len(video_grid_thw), dtype=torch.float32)
+            second_per_grid_ts = 2.0
+            second_per_grids = (
+                torch.ones(len(video_grid_thw), dtype=torch.float32)
+                * second_per_grid_ts
+            )
         else:
             second_per_grids = torch.tensor(second_per_grid_ts, dtype=torch.float32)