An apparatus for positioning a transport system and a load port is described, including a signal emitting unit disposed on the transport system and a positioning board on the load port. The signal emitting unit has two positioning points thereon capable of emitting two light beams to the positioning board, while the positioning board has two holes thereon at two positions corresponding to the two positioning points. The two light beams can pass through the two holes perpendicular to the positioning board in a horizontal state when the load port is aligned with the transport system.