Characteristics of droplet and film water motion in the flow channels of polymer electrolyte membrane fuel cells (PEMFCs) have important influence to cell performance, but the moving mechanism is not clear. Considering for the first time the hydrophilicity of graphite plate (GP) and the hydrophobicity of the gas diffusion layer (GDL), which form the walls of the gas channel, using the volume-of-fluid (VOF) model of FLUENT software, the motion of liquid water under different Weber numbers (or different gas velocities) was simulated in a straight channel and a serpentine channel. The results show that the hydrophilicity of GP and the hydrophobicity of GDL play an important role in the liquid water motion; the more hydrophobic the surfaces of the channel are, the more easily the water is to be discharged. Liquid water can be attracted from GDL onto the hydrophilic walls of the GP, which is beneficial to the diffusion of oxygen from the gas channel to the catalyst layer. When Weber number is larger than 4.4 (gas velocity is lower than 4 m s−1), effects of surface tension and wall surface adhesion on the motion of liquid water in the gas channel are very obvious; when Weber number is less than 4.4 (gas velocity is higher than 4 m s−1), inertia force plays the main role in the motion of liquid water in the gas channel. Liquid water is easier to be discharged under high velocity than under lower velocity, and in the straight channel than in the serpentine channel.