The invention provides a wiper control system which can control wiper arms to return accurately and reliably and a control method thereof. The wiper control system comprises a controller and a wiper motor, wherein the controller comprises a timing unit, the controller is connected with a mode selection switch and a reset switch, a first output end of the controller controls a mode relay, a second output end controls a power supply relay, a moving contact of the mode relay is connected with the moving contact of the power supply relay, two static contacts of the mode relay are respectively connected with a low-speed switch and a high-speed switch of the wiper motor, two static contacts of the power supply relay are respectively connected with a power supply and the ground, and the wiper motor is further grounded through a ground pin of the wiper motor. The controller comprises the timing unit and can determine the time delay of a wiper through theoretical calculation and vehicle parameter matching, carry out timing according to the time delay, disconnect the power supply relay at the appropriate time and brake the back-eletromotive force of the wiper motor, thereby returning the wiper arms accurately and reliably.