Disclosed is a control method of an air conditioner system for a vehicle. The air conditioner system is integrated with a cooling system and includes a water-cooled condenser embedded in an intercooler radiator and an air-cooled condenser placed in front of the intercooler radiator. The control method may include (A) circulating the refrigerant in the air conditioner system through actuation of a compressor by sensing actuation of an air conditioner while driving the vehicle in a state in which the start of the vehicle is on, (B) actuating a water pump circulating the cooling water and a cooling fan blowing wind to a cooling module, and (C) controlling the actuation of the compressor by judging whether the vehicle is in a failure mode in a state where the air conditioner is actuated or normally driving the compressor and the cooling fan and ending the control.