An air conditioning system for hybrid vehicles includes: a heater core receiving engine cooling water from an engine and heat an air blown into a vehicle room; an electric water pump pumping the engine cooling water through the heater core when a motor vehicle is switched from an engine drive mode to a motor drive mode; a discharged air temperature sensing unit sensing a discharged air temperature as a temperature of an air discharged into the vehicle room; and a control unit when the motor vehicle is switched from the engine drive mode to the motor drive mode differentially controls a rotational speed of the electric water pump depending on a temperature difference between the discharged air temperature inputted from the discharged air temperature sensing unit and a target discharge temperature calculated in advance based on internal/external temperature conditions and a user set temperature.