diff --git a/python/dgl/graphbolt/minibatch.py b/python/dgl/graphbolt/minibatch.py
index aef6b31988a2..f75c72ab005c 100644
--- a/python/dgl/graphbolt/minibatch.py
+++ b/python/dgl/graphbolt/minibatch.py
@@ -500,7 +500,7 @@ def to_pyg_data(self):
             col_nodes = torch.cat(col_nodes)
             row_nodes = torch.cat(row_nodes)
             edge_index = torch.unique(
-                torch.stack((col_nodes, row_nodes)), dim=1
+                torch.stack((row_nodes, col_nodes)), dim=1
             )
 
         if self.node_features is None:
diff --git a/tests/python/pytorch/graphbolt/test_minibatch.py b/tests/python/pytorch/graphbolt/test_minibatch.py
index 1f708c84c664..7a428fd828d9 100644
--- a/tests/python/pytorch/graphbolt/test_minibatch.py
+++ b/tests/python/pytorch/graphbolt/test_minibatch.py
@@ -881,7 +881,7 @@ def test_to_pyg_data():
         original_column_node_ids=torch.tensor([10, 11]),
     )
     expected_edge_index = torch.tensor(
-        [[0, 0, 1, 1, 1, 2, 2, 3], [0, 1, 0, 1, 2, 1, 2, 2]]
+        [[0, 0, 1, 1, 1, 2, 2, 2], [0, 1, 0, 1, 2, 1, 2, 3]]
     )
     expected_node_features = torch.tensor([[1], [2], [3], [4]])
     expected_labels = torch.tensor([0, 1])