A control method of an air conditioner system for an electric vehicle may include circulating the refrigerant by sensing actuation of the air conditioner system while driving the electric vehicle in a state where a start of the electric vehicle is turned on, circulating and cooling the cooling water through actuation of a water pump and a cooling fan in a cooling module that includes an engine radiator, the intercooler radiator, the water-cooled condenser, and the air-cooled condenser, and controlling actuation speeds of the water pump and the cooling fan based on whether the electric vehicle stops after suddenly accelerating in a state where the air conditioner system is actuated or stops in a state where the air conditioner system is turned off after travelling, and/or based on whether an air conditioner pressure and a cooling water temperature are within predetermined set values.