A method for dehydrating an evaporator of an air conditioner of a vehicle is provided to drive a blower motor depending on the humidity of the evaporator while monitoring a dry state of the evaporator, thus allowing the evaporator to be appropriately dried and preventing a problem from being caused by the discharge of a battery, therefore minimizing an odor generated by the air conditioner of the vehicle owing to effective drying of the evaporator of the air conditioner, and consequently considerably improving the marketability of the vehicle.