The present disclosure provides a system and a method for controlling a semiconductor manufacturing apparatus. The system includes an inspection unit capturing at least one image of a wafer, a sensor interface generating at least one input signal for a database server, and a control unit. The control unit includes a front-end subsystem, a calculation subsystem, and a message and tuning subsystem. The front-end subsystem receives the at least one input signal from the database server and performs a front-end process to generate a data signal. The calculation subsystem performs an artificial intelligence analytical process to determine, according to the data signal, whether damage marks have been caused by the semiconductor manufacturing apparatus and to generate an output signal. The message and tuning subsystem generates an alert signal and a feedback signal according to the output signal and transmits the alert signal to a user.