diff --git a/src/llamafactory/data/processor/supervised.py b/src/llamafactory/data/processor/supervised.py
index 25eb82adb..cc7bf3a96 100644
--- a/src/llamafactory/data/processor/supervised.py
+++ b/src/llamafactory/data/processor/supervised.py
@@ -61,7 +61,8 @@ class SupervisedDatasetProcessor(DatasetProcessor):
         input_ids, labels = self.template.mm_plugin.process_token_ids(
             [], [], images, videos, audios, self.tokenizer, self.processor
         )
-        encoded_pairs = self.template.encode_multiturn(self.tokenizer, messages, system, tools)
+        discarding_history_cot = self.data_args.mask_history and not self.template.preserve_thinking
+        encoded_pairs = self.template.encode_multiturn(self.tokenizer, messages, system, tools, discarding_history_cot)
         total_length = len(input_ids) + (1 if self.template.efficient_eos else 0)
         if self.data_args.mask_history:
             encoded_pairs = encoded_pairs[::-1]  # high priority for last turns
diff --git a/src/llamafactory/data/template.py b/src/llamafactory/data/template.py
index ff592db05..c8b4b0007 100644
--- a/src/llamafactory/data/template.py
+++ b/src/llamafactory/data/template.py
@@ -79,6 +79,7 @@ class Template:
         messages: list[dict[str, str]],
         system: Optional[str] = None,
         tools: Optional[str] = None,
+        discarding_history_cot: bool = False, # only effect reasoning template
     ) -> list[tuple[list[int], list[int]]]:
         r"""Return multiple pairs of token ids representing prompts and responses respectively."""
         encoded_messages = self._encode(tokenizer, messages, system, tools)
@@ -441,14 +442,24 @@ class ReasoningTemplate(Template):
         messages: list[dict[str, str]],
         system: Optional[str] = None,
         tools: Optional[str] = None,
+        discarding_history_cot: bool = False,
     ) -> list[tuple[list[int], list[int]]]:
         messages = deepcopy(messages)
         if self.enable_thinking is False:  # remove all cot
             for i in range(1, len(messages), 2):
                 messages[i]["content"] = self.remove_thought(messages[i]["content"])
 
+        if discarding_history_cot:
+            for i in range(1, len(messages) - 2, 2):  # preserve the last cot
+                messages[i]["content"] = self.remove_thought(messages[i]["content"])
+
         encoded_messages = self._encode(tokenizer, messages, system, tools)
-        for i in range(0, len(messages), 2):
+        if discarding_history_cot:
+            turn_indices = [len(messages) - 2]
+        else:
+            turn_indices = range(0, len(messages), 2)
+
+        for i in turn_indices:
             if (
                 self.thought_words[0].strip() not in messages[i + 1]["content"]
                 and self.thought_words[1].strip() not in messages[i + 1]["content"]
@@ -2135,23 +2146,6 @@ register_template(
 )
 
 
-# copied from qwen3_5_nothink template
-register_template(
-    name="qwen3_6_nothink",
-    format_user=StringFormatter(slots=["<|im_start|>user\n{{content}}<|im_end|>\n<|im_start|>assistant\n"]),
-    format_assistant=StringFormatter(slots=["{{content}}<|im_end|>\n"]),
-    format_system=StringFormatter(slots=["<|im_start|>system\n{{content}}<|im_end|>\n"]),
-    format_function=FunctionFormatter(slots=["{{content}}<|im_end|>\n"], tool_format="qwen3_5"),
-    format_observation=StringFormatter(
-        slots=["<|im_start|>user\n<tool_response>\n{{content}}\n</tool_response><|im_end|>\n<|im_start|>assistant\n"]
-    ),
-    format_tools=ToolFormatter(tool_format="qwen3_5"),
-    stop_words=["<|im_end|>"],
-    replace_eos=True,
-    mm_plugin=get_mm_plugin(name="qwen3_vl", image_token="<|image_pad|>", video_token="<|video_pad|>"),
-)
-
-
 register_template(
     name="sailor",
     format_user=StringFormatter(slots=["<|im_start|>question\n{{content}}<|im_end|>\n<|im_start|>answer\n"]),
diff --git a/tests/data/test_template.py b/tests/data/test_template.py
index b9d9ab2d8..e44210804 100644
--- a/tests/data/test_template.py
+++ b/tests/data/test_template.py
@@ -181,6 +181,39 @@ def test_reasoning_encode_multiturn(cot_messages: bool, enable_thinking: bool):
         (prompt_str_1, answer_str_1, prompt_str_2, answer_str_2),
     )
 
+@pytest.mark.runs_on(["cpu", "mps"])
+@pytest.mark.parametrize("enable_thinking", [True, False, None])
+@pytest.mark.parametrize("discarding_history_cot", [True, False])
+def test_reasoning_encode_multiturn_discarding_history_cot(enable_thinking: bool, discarding_history_cot: bool):
+    tokenizer = AutoTokenizer.from_pretrained("Qwen/Qwen3-8B")
+    data_args = DataArguments(template="qwen3", enable_thinking=enable_thinking)
+    template = get_template_and_fix_tokenizer(tokenizer, data_args)
+    encoded_pairs = template.encode_multiturn(tokenizer, MESSAGES_WITH_THOUGHT, discarding_history_cot=discarding_history_cot)
+
+    prompt_str_1 = f"<|im_start|>user\n{MESSAGES_WITH_THOUGHT[0]['content']}<|im_end|>\n<|im_start|>assistant\n"
+    prompt_str_2 = f"<|im_start|>user\n{MESSAGES_WITH_THOUGHT[2]['content']}<|im_end|>\n<|im_start|>assistant\n"
+
+    if enable_thinking is False:
+        answer_str_1 = f"{MESSAGES[1]['content']}<|im_end|>\n"
+        answer_str_2 = f"{MESSAGES[3]['content']}<|im_end|>\n"
+        if discarding_history_cot:
+            prompt_str_2 = prompt_str_2 + "<think>\n\n</think>\n\n"
+        else:
+            prompt_str_1 = prompt_str_1 + "<think>\n\n</think>\n\n"
+            prompt_str_2 = prompt_str_2 + "<think>\n\n</think>\n\n"
+    else:
+        if discarding_history_cot:
+            answer_str_1 = f"{MESSAGES[1]['content']}<|im_end|>\n"
+        else:
+            answer_str_1 = f"{MESSAGES_WITH_THOUGHT[1]['content']}<|im_end|>\n"
+        answer_str_2 = f"{MESSAGES_WITH_THOUGHT[3]['content']}<|im_end|>\n"
+
+    _check_tokenization(
+        tokenizer,
+        (encoded_pairs[0][0], encoded_pairs[0][1], encoded_pairs[1][0], encoded_pairs[1][1]),
+        (prompt_str_1, answer_str_1, prompt_str_2, answer_str_2),
+    )
+
 
 @pytest.mark.runs_on(["cpu", "mps"])
 def test_jinja_template():