The invention provides a control system of an air conditioner for a vehicle and the vehicle. The control system of the air conditioner for the vehicle comprises an engine, a first clutch, a motor, a second clutch, an air conditioner controller and a mode detection device, wherein the air conditioner controller is used for receiving a first signal and controlling disengagement of the first clutch and engagement of the second clutch, so that the motor provides power for an air conditioner compressor; or the air conditioner controller receives a second signal, controls engagement of the first clutch and disengagement of the second clutch, thus, the engine provides power for the air conditioner compressor. The mode detection device is used for detecting the running state of the hybrid electric vehicle, sends the first signal when detecting that the hybrid electric vehicle is in a motor drive running mode only and sends the second signal when detecting that the hybrid electric vehicle is in an engine drive or hybrid power drive running mode. The technical scheme can well meet the air conditioner drive requirement of the hybrid electric vehicle.