The invention discloses a control system and a control method of load of a wind turbine generator. The control system comprises a fan control system, a brake control system, a converter control system, a blade control system, a yawing driven control system, a tower strain sensor, an air speed sensor, a wind direction sensor, a rotor speed sensor and a blade strain gage. The fan control system is respectively connected with the brake control system, the converter control system, the blade control system, the yawing driven control system, the tower strain sensor, the air speed sensor, the wind direction sensor, the rotor speed sensor and the blade strain gage through data lines. According to the control system, under the condition of large yawing error at high wind speed, the running mode of the wind turbine generator is changed through the fan control system so that the load of the wind turbine generator can be within a normal range, and the load of the wind turbine generator can be reduced. The control system reduces the load of the control system, decreases the risk of overload of the wind turbine generator and greatly reduces probability of accidents of the wind turbine generator.