A method of controlling an air conditioning system can select several airflow modes with one air conditioner. The method includes a mode check step that checks whether the number of airflows of the air conditioner decreases, a state check step that checks whether a blower is selected to a minimum air amount mode, and a minimum operation step that operates a blower motor with a minimum torque smaller than a minimum start torque, if the number of airflows of the air conditioner decreases and the blower is selected to the minimum air amount mode.