The invention relates to a fuel cell engine cooling system which comprises an inner circulation pipeline and an outer circulation pipeline which are connected through a pipeline, wherein the internalcirculation pipeline comprises a fuel cell stack, a heat exchanger, a cooling liquid pump and a deionization filter, the heat dissipation outlet end of the fuel cell stack is sequentially connected tothe heat exchanger, the cooling liquid pump and the deionization filter and returns to the heat dissipation inlet end of the fuel cell stack, and cooling liquid circularly flows in the pipeline. Theouter circulation pipeline comprises a heat exchanger, a four-way valve, a booster pump, a whole vehicle radiator and an expansion valve, wherein the heat absorption outlet end of the heat exchanger is sequentially connected with the four-way valve, the booster pump, the whole vehicle radiator and the expansion valve and returns to the heat absorption inlet end of the heat exchanger, and the phasechange coolant circularly flows in the outer circulation pipeline. Since the heat exchanger is introduced, a traditional single cooling loop is changed into a double-circulation cooling loop, so thatthe problems that an original system radiator is too large in area, a pipeline is too long, ion precipitation is difficult to control and the like are solved, the cooling effect is good, and the design cost of a cooling system is reduced.