The invention discloses a control system for a four-rotor aircraft. The control system comprises a master controller, an inertial measurement unit, a geomagnetometer, a distance measuring sensor, a GPS module, a camera module, an image processing unit, a motor drive module and four motors, wherein the inertial measurement unit, the geomagnetometer, the distance measuring sensor and the GPS module are connected with the master controller, the camera module is connected with the master controller through the image processing unit, the master controller is connected with the four motors through the motor drive module, and the four motors drive four airscrews of the four-rotor aircraft respectively. The invention further comprises a control method of the control system. The control method involves an attitude control algorithm, a height determination control algorithm and a data fusion algorithm. Data fusion of the inertial measurement unit and a positioning system is adopted for a control structure and the control method, and stability and reliability of the system are improved.