A screw locking control system includes a host, a control unit controlled by the host, an electric screw driver and a holder. The control unit includes a processor, a voltage detecting module, a power outlet for providing electricity to the electric screw driver, and a lighting signal control module electrically connected to a plurality of indicator lamps of the holder. As a result, the control unit can turn on the indicator lamps sequentially via the light signal control module, guiding operators to carry out each screw locking operation and detecting a voltage variance of the electric screw driver to determine whether each screw locking operation is qualified. Thus, the quality of the manufacturing process is consistently maintained.