Water management is a key issue for the performance of a polymer electrolyte membrane (PEM) fuel cell. Materials of the fuel cell would affect the water transportation in the flow field, thus influence, the overall performance of the fuel cell. A three dimensional, single-channel, counterflow model was built to analyze the performance of the PEM fuel cell. Different surface contact angles were set to the liquid water droplets in the catalyst layers (CLs) and gas diffusion layers (GDLs) to present the different wetting property characterizations of the materials. Assuming that the contact angle ranges from 75 deg to 150 deg, the liquid water content and distribution in the cathode GDL were investigated in details. Numerical analysis showed that the hydrophobicity of the structure affects the water transportation in the fuel cell significantly. Hydrophobic materials could lower the rate of water saturation in the flow field, thus preventing the water flooding in the cathode side. When the surface contact angles of the cathode CL and GDL were set to 135 deg, the liquid water content is least in the GDL. I-V polarization curves of the fuel cell with different materials were also developed to analyze the overall performance. As a result, proper hydrophobic material would lower the rate of cathode water flooding in PEM and benefit the performance of PEM fuel cell.