A compressed air cooling apparatus of a fuel cell system is provided that includes i) a heat absorber installed at a first part of an air supplying system which supplies compressed air of a first compressed by an air compressor to a fuel cell stack, ii) a heat radiator installed at a second part of a stack cooling system which cools a coolant circulating to the fuel cell stack, iii) a heat pipe which connects the heat absorber and the heat radiator and is filled with the refrigerant therein, wherein the heat absorber is disposed at a lower position than the heat radiator for the refrigerant to flow from the heat radiator to the heat absorber.