In this study a three-dimensional mathematical model is developed to simulate the flow field and mass transfer in a PEM fuel cell. In the model, the effects of the different flow channel structures in heterogeneous composite carbon fiber bipolar plates and traditional hard surface bipolar plates on the performance are studied. The results show that, the cell performance with the heterogeneous composite carbon fiber bipolar plates have better performance than that with the traditional hard surface bipolar plates, whether in the parallel flow channel structures or the serpentine flow channel structures. The reason is that, the heterogeneous composite carbon fiber ribs are porous material, so it allows the reactants and products transport uniformly even in the rib zone. This greatly improved the mass transfer and the gases distribution in the fuel cell. With the traditional bipolar plates, the reactants can only enter the reaction zone from the side of carbon cloth under ribs, so that the performance in this area under rib is relatively poor. In the simulation of the flow channel structures, we detect that, due to the single inlet serpentine flow channel have stronger convective effects that forced reactants to flow through the whole reaction zones, so it has better performance at high current density than in the singles inlet parallel flow channel. In addition, the results also show that, higher fuel stoichiometric number and operated pressure and properly humidified at anode will all improve the performance of the fuel cell.