diff --git a/docs/user_guide/examples/online_serving/qwen3_omni.md b/docs/user_guide/examples/online_serving/qwen3_omni.md
index e372692a8..b4c05bdbe 100644
--- a/docs/user_guide/examples/online_serving/qwen3_omni.md
+++ b/docs/user_guide/examples/online_serving/qwen3_omni.md
@@ -306,7 +306,7 @@ The gradio script supports the following arguments:
     ``````
 ??? abstract "qwen3_omni_moe_thinking.yaml"
     ``````yaml
-    --8<-- "examples/online_serving/qwen3_omni/qwen3_omni_moe_thinking.yaml"
+    --8<-- "vllm_omni/deploy/qwen3_omni_moe_thinking.yaml"
     ``````
 ??? abstract "run_curl_multimodal_generation.sh"
     ``````sh
diff --git a/examples/online_serving/qwen3_omni/qwen3_omni_moe_thinking.yaml b/examples/online_serving/qwen3_omni/qwen3_omni_moe_thinking.yaml
deleted file mode 100644
index 7ce88f80a..000000000
--- a/examples/online_serving/qwen3_omni/qwen3_omni_moe_thinking.yaml
+++ /dev/null
@@ -1,36 +0,0 @@
-# Stage config for running Qwen3-Omni-MoE-Thinking (text-only output)
-# This config is for models like Qwen3-Omni-30B-A3B-Thinking that only have the
-# thinker component and do not support audio output.
-#
-# Single stage: Thinker (multimodal understanding + text generation)
-
-# The following config has been verified on 2x H100-80G GPUs.
-stage_args:
-  - stage_id: 0
-    runtime:
-      devices: "0,1"
-    engine_args:
-      model_stage: thinker
-      max_num_seqs: 1
-      model_arch: Qwen3OmniMoeForConditionalGeneration
-      worker_type: ar
-      scheduler_cls: vllm_omni.core.sched.omni_ar_scheduler.OmniARScheduler
-      gpu_memory_utilization: 0.9
-      enforce_eager: true
-      trust_remote_code: true
-      engine_output_type: text
-      distributed_executor_backend: "mp"
-      enable_prefix_caching: true
-      hf_config_name: thinker_config
-      tensor_parallel_size: 2
-    final_output: true
-    final_output_type: text
-    is_comprehension: true
-    default_sampling_params:
-      temperature: 0.4
-      top_p: 0.9
-      top_k: 1
-      max_tokens: 2048
-      seed: 42
-      detokenize: True
-      repetition_penalty: 1.05
diff --git a/examples/online_serving/qwen3_omni/run_gradio_demo.sh b/examples/online_serving/qwen3_omni/run_gradio_demo.sh
index 73ce273d9..465304534 100755
--- a/examples/online_serving/qwen3_omni/run_gradio_demo.sh
+++ b/examples/online_serving/qwen3_omni/run_gradio_demo.sh
@@ -13,7 +13,7 @@ set -e
 MODEL="Qwen/Qwen3-Omni-30B-A3B-Instruct"
 SERVER_PORT=8091
 GRADIO_PORT=7861
-STAGE_CONFIGS_PATH=""
+DEPLOY_CONFIG=""
 SERVER_HOST="0.0.0.0"
 GRADIO_IP="127.0.0.1"
 GRADIO_SHARE=false
@@ -33,8 +33,8 @@ while [[ $# -gt 0 ]]; do
             GRADIO_PORT="$2"
             shift 2
             ;;
-        --stage-configs-path)
-            STAGE_CONFIGS_PATH="$2"
+        --deploy-config)
+            DEPLOY_CONFIG="$2"
             shift 2
             ;;
         --server-host)
@@ -56,7 +56,7 @@ while [[ $# -gt 0 ]]; do
             echo "  --model MODEL                 Model name/path (default: Qwen/Qwen3-Omni-30B-A3B-Instruct)"
             echo "  --server-port PORT            Port for vLLM server (default: 8091)"
             echo "  --gradio-port PORT            Port for Gradio demo (default: 7861)"
-            echo "  --stage-configs-path PATH     Path to custom stage configs YAML file (optional)"
+            echo "  --deploy-config PATH          Path to custom deploy config YAML file (optional)"
             echo "  --server-host HOST            Host for vLLM server (default: 0.0.0.0)"
             echo "  --gradio-ip IP                IP for Gradio demo (default: 127.0.0.1)"
             echo "  --share                       Share Gradio demo publicly"
@@ -87,8 +87,8 @@ echo "=========================================="
 
 # Build vLLM server command
 SERVER_CMD=("vllm" "serve" "$MODEL" "--omni" "--port" "$SERVER_PORT" "--host" "$SERVER_HOST")
-if [ -n "$STAGE_CONFIGS_PATH" ]; then
-    SERVER_CMD+=("--stage-configs-path" "$STAGE_CONFIGS_PATH")
+if [ -n "$DEPLOY_CONFIG" ]; then
+    SERVER_CMD+=("--deploy-config" "$DEPLOY_CONFIG")
 fi
 
 # Function to cleanup on exit
diff --git a/tests/config/test_config_factory.py b/tests/config/test_config_factory.py
index 3e482f48f..a811868c1 100644
--- a/tests/config/test_config_factory.py
+++ b/tests/config/test_config_factory.py
@@ -1233,6 +1233,45 @@ stages:
         assert deploy.connectors is not None
         assert deploy.platforms is not None
 
+    def test_qwen3_omni_thinker_only_deploy_config_uses_resolved_pipeline(self):
+        deploy_path = Path(get_deploy_config_path("qwen3_omni_moe_thinking.yaml"))
+        with patch(
+            "vllm_omni.config.config_factory.get_config",
+            return_value=Q3_OMNI_THINKER_HF_CONFIG,
+        ):
+            pipeline = StageConfigFactory.get_pipeline_config(
+                "Qwen/Qwen3-Omni-30B-A3B-Thinking",
+                trust_remote_code=False,
+                deploy_config_path=str(deploy_path),
+            )
+
+        assert pipeline is not None
+        assert pipeline.model_type == "qwen3_omni_moe_thinker_only"
+
+        deploy = load_deploy_config(deploy_path)
+        stages = merge_pipeline_deploy(pipeline, deploy)
+
+        assert len(stages) == 1
+        thinker = stages[0]
+        assert thinker.model_stage == "thinker"
+        assert thinker.final_output is True
+        assert thinker.final_output_type == "text"
+        assert thinker.worker_type == "ar"
+        assert thinker.scheduler_cls == "vllm_omni.core.sched.omni_ar_scheduler.OmniARScheduler"
+        assert thinker.hf_config_name == "thinker_config"
+        assert thinker.is_comprehension is True
+        assert thinker.yaml_runtime["devices"] == "0,1"
+        assert thinker.yaml_engine_args["engine_output_type"] == "text"
+        assert thinker.yaml_engine_args["tensor_parallel_size"] == 2
+        assert thinker.yaml_engine_args["max_num_seqs"] == 1
+        assert thinker.yaml_engine_args["gpu_memory_utilization"] == 0.9
+        assert thinker.yaml_engine_args["enforce_eager"] is True
+        assert thinker.yaml_engine_args["async_scheduling"] is False
+        assert thinker.yaml_engine_args["distributed_executor_backend"] == "mp"
+        assert thinker.yaml_engine_args["enable_prefix_caching"] is True
+        assert thinker.yaml_engine_args["async_chunk"] is False
+        assert thinker.yaml_extras["default_sampling_params"]["detokenize"] is True
+
     def test_load_voxtral_tts_deploy_config_schema_fields(self):
         deploy_path = Path(get_deploy_config_path("voxtral_tts.yaml"))
         deploy = load_deploy_config(deploy_path)
diff --git a/vllm_omni/deploy/qwen3_omni_moe_thinking.yaml b/vllm_omni/deploy/qwen3_omni_moe_thinking.yaml
new file mode 100644
index 000000000..7ccc64750
--- /dev/null
+++ b/vllm_omni/deploy/qwen3_omni_moe_thinking.yaml
@@ -0,0 +1,21 @@
+# Deploy config for Qwen3-Omni-MoE thinker-only checkpoints.
+# Verified on 2x H100-80G GPUs.
+pipeline: qwen3_omni_moe
+distributed_executor_backend: mp
+enable_prefix_caching: true
+
+stages:
+  - stage_id: 0
+    devices: "0,1"
+    max_num_seqs: 1
+    gpu_memory_utilization: 0.9
+    enforce_eager: true
+    async_scheduling: false
+    tensor_parallel_size: 2
+    default_sampling_params:
+      temperature: 0.4
+      top_p: 0.9
+      top_k: 1
+      max_tokens: 2048
+      seed: 42
+      repetition_penalty: 1.05
diff --git a/vllm_omni/model_executor/models/qwen3_omni/pipeline.py b/vllm_omni/model_executor/models/qwen3_omni/pipeline.py
index 9baecdd3e..c93e764ef 100644
--- a/vllm_omni/model_executor/models/qwen3_omni/pipeline.py
+++ b/vllm_omni/model_executor/models/qwen3_omni/pipeline.py
@@ -88,7 +88,7 @@ QWEN3_OMNI_THINKER_ONLY_PIPELINE = PipelineConfig(
             owns_tokenizer=True,
             requires_multimodal_data=True,
             hf_config_name="thinker_config",
-            engine_output_type="latent",
+            engine_output_type="text",
             sampling_constraints={"detokenize": True},
         ),
     ),