An air intake method and system of an air conditioner for a vehicle may include a temperature measuring step, a speed sensing step, a blower sensing step, and a simultaneous indoor and outdoor air intake step. The air intake system includes a water temperature sensor for measuring the temperature of cooling water of the vehicle, a speed sensor for measuring the speed of the vehicle, a control switch for turning on or off a blower, a control unit and an intake actuator. The control unit receives the temperature measured by the water temperature sensor, the speed measured by the speed sensor and ON/OFF data from the control switch, thus determining whether to simultaneously draw indoor and outdoor air in or not. The intake actuator provides driving force so that an indoor and outdoor air control door simultaneously opens indoor and outdoor air inlets.