diff --git a/pyscf/pbc/df/ft_ao.py b/pyscf/pbc/df/ft_ao.py
index 2fb27f2180..a1a1e14c56 100644
--- a/pyscf/pbc/df/ft_ao.py
+++ b/pyscf/pbc/df/ft_ao.py
@@ -632,21 +632,23 @@ def strip_basis(self, rcut):
         dim = rs_cell.dimension
         if dim == 0:
             return self
-        supmol_bas_coords = self.atom_coords()[self._bas[:,gto.ATOM_OF]]
-        rb = np.linalg.norm(supmol_bas_coords[:,:dim], axis=1)
-        a = rs_cell.lattice_vectors()
+
+        # Search the shortest distance to the reference cell for each atom in the supercell.
+        atom_coords = self.atom_coords()
+        d = np.linalg.norm(atom_coords[:,None] - rs_cell.atom_coords(), axis=2)
+        shortest_dist = np.min(d, axis=1)
+        bas_dist = shortest_dist[self._bas[:,gto.ATOM_OF]]
 
         # filter _bas
         nbas0 = self._bas.shape[0]
-        if rb.size == self.bas_mask.size:
-            dr = rb - np.linalg.norm(a[:dim])
-            dr = dr.reshape(self.bas_mask.shape)
-            self.bas_mask = bas_mask = dr < rcut[:,None]
+        if bas_dist.size == self.bas_mask.size:
+            bas_dist = bas_dist.reshape(self.bas_mask.shape)
+            self.bas_mask = bas_mask = bas_dist < rcut[:,None]
             self._bas = self._bas[bas_mask.ravel()]
         else:
             dr = np.empty(self.bas_mask.shape)
             dr[:] = 1e9
-            dr[self.bas_mask] = rb - np.linalg.norm(a[:dim])
+            dr[self.bas_mask] = bas_dist
             bas_mask = dr < rcut[:,None]
             self._bas = self._bas[bas_mask[self.bas_mask]]
             self.bas_mask = bas_mask