In order to solve problems like the decline of energy efficiency of cells, or the large temperature difference in the outlet and inlet of electric piles, which are caused by unstable temperature during the operation of PEM fuel cells, the authors established models in the simulation software—Simcenter AMESim, such as the electric piles of fuel cells, automobiles, drivers, engines, and gas supply, so the performance of fuel cells could be studied. The authors also adopted a Fuzzy PID controller, which was compared to the traditional PID controller in terms of control effects under the operating conditions of the New European Driving Cycle (NEDC). The comparison and analysis results reveal that a water & heat management system adopting a Fuzzy PID controller could better adjust the temperature & humidity of cells, keep the temperature difference between the outlet and inlet of electric piles under 3°C, and raise the output voltage by 2.35%. The results of this study can, to some extent, serve as the basis for other studies on PEM fuel cells.