Hi Ming-Chou,
Many points overlap exactly so changing point size is not going to help.
Complement[a, b]
(* {{24.9868, 121.309}, {24.9954, 121.304}} *)
Complement[b, a]
(* {{24.9948, 121.32}} *)
If the points are close then maybe DynamicGeoGraphics will work. The user can pan and zoom to see the close points.
DynamicGeoGraphics[{PointSize[0.01], Red, Point@GeoPosition@a, Blue, Point@GeoPosition@b},
GeoZoomLevel -> 11]
