The instant disclosure provides a method for operating an automatic handling system applied to many wafer processing apparatuses. When a OHT (Overhead Hoist Transport) vehicle is moved to one of the wafer processing apparatuses, the OHT vehicle can ask a OHT control module whether a wafer carrier device can be unloaded from the OHT vehicle onto the wafer processing apparatus. There are two judgment methods as follows: (1) If there is another wafer carrier device already disposed on the wafer processing apparatus, the OHT control module will inform the OHT vehicle that the wafer carrier device cannot be unloaded from the OHT vehicle onto the wafer processing apparatus; (2) If there is no any wafer carrier device disposed on the wafer processing apparatus, the OHT control module will inform the OHT vehicle that the wafer carrier device can be unloaded from the OHT vehicle onto the wafer processing apparatus.