Hi SUIYAN, it's because boolean union will merge together surfaces that are trimmed pieces of the same "underlying surface".

You can see the difference between those 2 cases by turning on surface control points using Edit > Show pts.

If you turn on points for your first case, you should see that the underlying surfaces are each a sphere but they are not identical surfaces because they have different rotations:


If you turn on surface control points for the other case where the faces get merged, you should see the "underlying surfaces" of the 2 pieces are identical:


If you do not wish for surfaces to be merged, you can use Edit > Join instead of boolean union.

- Michael