An overhead wafer transport system includes an over head transportation (OHT) rail and at least one shuttle. The OHT rail includes a main track and two lateral tracks, each having a hollow transverse cross-section, each lateral track being in corresponding connection with the main track through the two sides thereof, constituting an approximate tri-directional branch form. The shuttle has a track-interface assembly and a docking unit, the track-interface assembly being adapted to travel along the OHT rail. The track-interface assembly being arranged at the junction of the two lateral tracks and the main track, wherein the track-interface assembly is adapted to selectively travel along at least one of the main track and the lateral tracks. Therefore, the overhead wafer transport system can be applied to a clean room with higher transfer efficiency and clean room space utilization.