The invention provides an air freshener generating apparatus of a vehicle air conditioning system adapted to generate and discharge different sorts of air fresheners filled within a cartridge into an interior of a vehicle. The air freshener generating apparatus of a vehicle air conditioning system includes: a body in which an inlet pipe is communicated with an outlet pipe and on which ball plungers are mounted at intervals on a circumferential surface thereof along circumferential lines on which the inlet pipe and the outlet pipe are located respectively; a cartridge coupled to the body and having at least one partition wall such that at least two air fresheners are filled within spaces defined by the partition wall, the cartridge having through-holes at portions of the cartridge corresponding to the spaces defined by the partition wall; and an actuator configured to rotate the cartridge a predetermined angle. When the cartridge is rotated the predetermined angle, air is supplied through the through-hole facing the inlet pipe such that one air freshener is discharged through the through-hole facing the outlet pipe without being mixed with another air freshener.