diff --git a/dpdata/system.py b/dpdata/system.py
index a777ccb6..18b16aaf 100644
--- a/dpdata/system.py
+++ b/dpdata/system.py
@@ -370,10 +370,10 @@ def map_atom_types(
         _set2 = set(list(type_map.keys()))
         assert _set1.issubset(_set2)
 
-        atom_types_list = []
-        for name, numb in zip(self.get_atom_names(), self.get_atom_numbs()):
-            atom_types_list.extend([name] * numb)
-        new_atom_types = np.array([type_map[ii] for ii in atom_types_list], dtype=int)
+        atom_names = self.get_atom_names()
+        new_atom_types = np.array(
+            [type_map[atom_names[ii]] for ii in self.data["atom_types"]], dtype=int
+        )
 
         return new_atom_types
 
diff --git a/tests/test_system_set_type.py b/tests/test_system_set_type.py
index d8362ec7..58bc0cdc 100644
--- a/tests/test_system_set_type.py
+++ b/tests/test_system_set_type.py
@@ -6,6 +6,24 @@
 from context import dpdata
 
 
+class TestMapAtomTypes(unittest.TestCase):
+    def test_map_atom_types_preserves_current_atom_order(self):
+        data = {
+            "atom_names": ["O", "H"],
+            "atom_numbs": [1, 2],
+            "atom_types": np.array([1, 0, 1]),
+            "orig": np.zeros(3),
+            "cells": np.eye(3).reshape(1, 3, 3),
+            "coords": np.zeros((1, 3, 3)),
+        }
+
+        system = dpdata.System(data=data)
+
+        np.testing.assert_array_equal(
+            system.map_atom_types({"H": 0, "O": 1}), np.array([0, 1, 0])
+        )
+
+
 class TestSetAtomTypes(unittest.TestCase):
     def setUp(self):
         self.system_1 = dpdata.LabeledSystem("poscars/vasprun.h2o.md.10.xml")