Nanofluids have high thermal conductivity and electrical conductivity, and there is a problem of electrical discharge when used as a coolant in proton exchange membrane fuel cell (PEMFC). In this study, the compact Al2O3 insulating coating was prepared by supersonic plasma spray processing technology and evenly coated in the cooling channel. The electrical discharge effect and heat transfer enhancement ability of three coolants, namely deionized water, Al2O3 nanofluid and graphene nanofluid, were studied when applied in the electrically active atmosphere of PEMFC. The results show that, the graphene nanofluid has the best heat transfer performance before insulation coating integration, but the dispersion of solid nanoparticles in the base fluid leads to a higher pressure drop, with an increase of 6.7%. When the voltage is 200 V, the leakage current of Al2O3 nanofluid and graphene nanofluid is up to 16 mA and 33 mA respectively. After insulation coating integration, the index of uniform temperature (IUT) and maximum temperature of graphene nanofluids further decrease, while the pressure drop increases by 7.0%. The leakage current of all three coolants at different voltages and Re numbers decrease to 0, indicating a significant improvement in the insulation performance of PEMFC cooling channel. In addition, dimensionless evaluation parameter ε for the applicability of heat transfer fluids were proposed from the perspectives of work and energy. Within the pump power range of 0.0065 W ∼ 0.0325 W, the ε of graphene nanofluids with insulating coating is always lower than Al2O3 nanofluid. At the pump power of 0.014 W, the ε of graphene nanofluids with insulating coating is 0.76, which has the best coolant applicability when applied in the electrically active atmosphere of PEMFC.