The present invention relates to a method for controlling an air conditioner for a vehicle, which includes a blower having a structure divided into a plurality of inlets and a plurality of outlets. The method may include: detecting or predicting, by a controller, one or more of an inside temperature of the vehicle, an outside temperature, a temperature of an engine serving as a heating source, an indoor humidity of the vehicle, CO2 concentration and rear seat passenger information; and comprehensively determining, by the controller, an outdoor state of the vehicle, an indoor state of the vehicle and a user's intention based on the detected or predicted information and a blower setting mode, and controlling an inlet door of the air conditioner according to one of a plurality of designated steps.