A vehicle apparatus control system and method thereof are disclosed. The vehicle apparatus control system comprises a data storage module, an image capturing module, a face recognition module and a control module. The data storage module stores multiple registered users' facial feature parameters and vehicle apparatus setting parameters, and integration setting data. The face recognition module detects several facial images contained in the captured image and recognizes the users corresponding to the face images according to the facial feature parameters stored in data storage module. The control module set a vehicle apparatus according to the integration setting data, and the corresponding users' vehicle apparatus setting parameters.