diff --git a/monai/bundle/reference_resolver.py b/monai/bundle/reference_resolver.py
index 710bb399ae..7b74263d65 100644
--- a/monai/bundle/reference_resolver.py
+++ b/monai/bundle/reference_resolver.py
@@ -222,6 +222,9 @@ def update_refs_pattern(cls, value: str, refs: dict) -> str:
         """
         # regular expression pattern to match "@XXX" or "@XXX#YYY"
         result = cls.id_matcher.findall(value)
+        # reversely sort the matched references by length
+        # and handle the longer first in case a reference item is substring of another longer item
+        result.sort(key=len, reverse=True)
         value_is_expr = ConfigExpression.is_expression(value)
         for item in result:
             # only update reference when string starts with "$" or the whole content is "@XXX"
diff --git a/tests/test_config_parser.py b/tests/test_config_parser.py
index 9c7701e9fa..c4b50daed1 100644
--- a/tests/test_config_parser.py
+++ b/tests/test_config_parser.py
@@ -107,6 +107,8 @@ def __call__(self, a, b):
 
 TEST_CASE_4 = [{"A": 1, "B": "@A", "C": "@D", "E": "$'test' + '@F'"}]
 
+TEST_CASE_5 = [{"training": {"A": 1, "A_B": 2}, "total": "$@training#A + @training#A_B + 1"}, 4]
+
 
 class TestConfigParser(unittest.TestCase):
     def test_config_content(self):
@@ -296,6 +298,11 @@ def test_builtin(self):
         config = {"import statements": "$import math", "calc": {"_target_": "math.isclose", "a": 0.001, "b": 0.001}}
         self.assertEqual(ConfigParser(config).calc, True)
 
+    @parameterized.expand([TEST_CASE_5])
+    def test_substring_reference(self, config, expected):
+        parser = ConfigParser(config=config)
+        self.assertEqual(parser.get_parsed_content("total"), expected)
+
 
 if __name__ == "__main__":
     unittest.main()