diff --git a/swift/template/template_meta.py b/swift/template/template_meta.py
index 7a8b6dcb3b..7e7a5e171c 100644
--- a/swift/template/template_meta.py
+++ b/swift/template/template_meta.py
@@ -69,7 +69,7 @@ def _has_system(prefix_or_prompt: Prompt) -> bool:
 
     @staticmethod
     def _replace_system(prefix: Prompt) -> Prompt:
-        return [p.replace('{{SYSTEM}}', '') for p in prefix if isinstance(p, str)]
+        return [p.replace('{{SYSTEM}}', '') if isinstance(p, str) else p for p in prefix]
 
     def _check_template_meta(self):
         # check
diff --git a/tests/general/test_template_meta.py b/tests/general/test_template_meta.py
new file mode 100644
index 0000000000..58d8757e29
--- /dev/null
+++ b/tests/general/test_template_meta.py
@@ -0,0 +1,22 @@
+# Copyright (c) ModelScope Contributors. All rights reserved.
+from swift.template import TemplateMeta
+
+
+def test_replace_system_preserves_non_string_elements():
+    """_replace_system must not drop list elements like ['bos_token_id'].
+
+    Templates such as ziya, bluelm and emu3_chat use
+    ``prefix=[['bos_token_id'], '{{SYSTEM}}']``.  When no system message is
+    provided the prefix is produced by _replace_system, which should keep every
+    non-string element intact and only strip the placeholder from strings.
+    """
+    meta = TemplateMeta(
+        template_type='_test_replace_system_bug',
+        prefix=[['bos_token_id'], '{{SYSTEM}}'],
+        prompt=['{{QUERY}}'],
+        chat_sep=['\n'],
+    )
+    # __post_init__ moves prefix to system_prefix and builds a no-system prefix
+    # via _replace_system.  The list element must survive.
+    assert any(isinstance(p, list) for p in meta.prefix), (f'_replace_system dropped the bos_token_id list; '
+                                                           f'meta.prefix={meta.prefix!r}')