The invention discloses a fuel vehicle air conditioner control system. The system comprises an air conditioner controller, a battery management module, a vehicle battery pack, an electric generator, an electric compressor, an air blowing motor and a condensation fan. The battery management module is electrically connected with the air conditioner controller and the vehicle battery pack, and the air conditioner controller is used for obtaining the state of an engine when an air conditioner is started and sending a control signal to the battery management module; the battery management module controls the power supply state of the vehicle battery pack according to the control signal; the electric compressor is electrically connected with a first relay and the vehicle battery pack to form a first air conditioner power supply circuit which is in signal connection with the air conditioner controller; the electric generator is electrically connected with a second relay and the vehicle battery pack, and a charging circuit is formed; the air blowing motor and the condensation fan are connected with the vehicle battery pack through a third relay, and a second air conditioner power supply circuit is formed; and the air blowing motor and the condensation fan are electrically connected with the electric generator. The production cost of a whole vehicle can be reduced.