Proton exchange membrane fuel cell (PEMFC) reaction byproduct water is eventually discharged from the cathode channel through the surface of the diffusion layer (GDL). Although there are many studies on the kinetic behavior of liquid water in the cathode flow channel, there is still a lack of literature on water transport behavior in the flow channel considering the pore structure distribution on the GDL surface. In this paper, the effect of different size liquid water inlet arrangements on the GDL surface on the water management performance of the cathode runner is investigated. The volume of fluid (VOF) model is used to simulate the gas-liquid two-phase flow phenomenon in the channel. The results show that the droplet size discharged from the cathode flow channel is basically the uniformity when the liquid water inlet is distributed in gas flow from the largest to the smallest in size. At the same time, the maximum total liquid water content achievable in the flow channel, the maximum GDL surface coverage is the smallest, and the cathode flow channel has the best water management performance. The effect of pore structure distribution on the surface of GDL should be considered when conducting the study of water transport behavior in the cathode flow channel to reveal further the transport process of liquid water in the cathode channel and the removal mechanism.