The water management of proton-exchange membrane fuel cell (PEMFC) has a major impact on the performance of the cell system. In order to investigate the influence of air velocity and wettability on the whole process during penetration of liquid water, a generalized two-dimensional modelin conjunction with the volume of fluid (VOF) method was used to simulate the whole processes from gas diffusion layer (GDL) to gas channel (GC). The results show that the wettability of the medium plays a significant role than flow rate for the penetration of liquid water in the GDL. It is shown that favorable hydrophobicity and high air velocity in GC is helpful to remove liquid droplets on the GDL surface. By contrast, the stable droplets spacing on GDL surface is more concentrated and the percentage of liquid area is more extensive under the hydrophilic and low-velocity case, which would aggravate the liquid water and hard to remove from the GDL surface.