The invention provides an auto air-conditioner control system and a control method thereof, and aims to satisfy the requirements of security and comfort. The system comprises an air-conditioner control unit. The air-conditioner control unit receives signals from an internal temperature sensor, a sunlight sensor, an external temperature sensor, an air quality sensor and an evaporator temperature sensor and sends control commands to control the work of an electric velocity modulation module, a blower, an internal and external throttle actuator, a mixture throttle actuator, a pattern throttle actuator and a defrosting throttle actuator, especially the air-conditioner control unit is connected with a front body electronic control system and an engine electronic injection control system through a CAN bus; and the air-conditioner control unit adjusts the work of the air condition system through the state information of the front body electronic control system and the engine electronic injection control system. The system optimizes circuit design, simplifies the operation procedure, satisfies the comfort requirement of a driver, and improves maintenance convenience and the reliability and safety of the system.