Due to its advantages of high efficiency, high power density at low temperature, fast start-up and zero emission, fuel cells are of great significance in automobile drive application. A car powered by electricity generated by an on-board fuel cell device is called a fuel cell vehicle (FCV). Fuel cells have a large demand for heat dissipation, and the layout space of automotive cooling modules is limited. Based on this situation, a parallel arrangement of multiple radiators is proposed. Using numerical simulation means to verify and optimize the designed multiple circuits cooling system (MCCS), from the original layout scheme based on the Taguchi method to establish the objective function of the reliability design of the MCCS, select A2/B1/C1/D2/E1/F1. In the scheme, the outlet temperature of the fuel cell is finally reduced to 75.8 °C. The cooling performance is improved, and the spatial layout of the individual cooling components can also be optimized. The whole vehicle experiment was carried out under four working conditions of full power idling charging, half power idling charging, constant speed of 40 km/h and constant speed of 80 km/h, to verify the cooling performance of the MCCS and to prove the effectiveness of the MCCS designed in this paper.