An air conditioning system of a vehicle includes a body, an electric heater core installed within the body and configured to generate a hot air, a cooling device installed within the body and configured to generate a cold air, and a control device configured to control a temperature of the hot air generated by the electric heater core or a temperature of the cold air generated by the cooling device, respectively, by controlling an amount of current applied to the electric heater core or the cooling device according to a difference between an internal temperature or an external ambient temperature of the vehicle and a target temperature, the electric heater core and the cooling device being operated independently of each other.