The flow channel design of the fuel cell has a great influence on the performance of proton exchange membrane fuel cell (PEMFC). Serpentine flow channel is widely applied because of its excellent performance among different channel designs. In this work, a multiphase, 3D PEMFC model with serpentine flow channel is developed. This work has analysed current density, relative pressure drop, velocity of reactants, oxygen concentrations, distribution of liquid water and temperature. The results show that the change of the cross-section in the serpentine flow channel can increase the current density of the PEMFC, while it also reduces the uniformity of the current density distribution. In this work, the oxygen is more concentrated and more reaction heat is generated when the cross-sectional shape of the flow channel changes from a trapezoid to a triangle, therefore the current density is higher in this case.