An air conditioning system for motor vehicles includes a temperature door configured to adjust an opening degree of a hot air path, a PTC heater configured to heat an air introduced into the hot air path, and a control unit configured to control an opening position of the temperature door with respect to the hot air path and to secure a minimum opening degree of the hot air path, so that a minimum amount of air is blown toward the PTC heater regardless of the opening position of the temperature door. The control unit is configured to actively adjust the minimum opening degree of the hot air path depending on an on/off condition of the PTC heater.