Proton exchange membrane fuel cells have a development prospect to replace the internal combustion engines due to their sustainability and environmental friendliness. However, one of the challenges is the requirement of heat removal from fuel cell engines and keep operation at relatively low temperatures (ie,~60 C-80 C). In the current research, the thermal performance of zinc oxide (ZnO) and boron nitride (BN) nanofluids is investigated by numerical simulation inside the engine compartment for a fuel cell vehicle. The maximum heat transfer rate was obtained by theoretical calculation and onedimensional simulation. The results revealed that the maximum heat transfer rate for ZnO nanofluids and BN nanofluids had increased by 7.6% and 2.0% than 50% water and ethylene glycol (WEG), respectively. Compared to 50% WEG, the energy consumption of the pump and fan could be further reduced with the nanofluids as a coolant. The influence on the temperature field and flow field inside the engine compartment of fuel cell vehicle is revealed with nanofluids by computational fluid dynamic. The results could provide data for the manufacturers to use nanofluids as a coolant to optimize the structure arrangement inside the engine compartment of fuel cell vehicle.