The structure of the gas diffusion layer (GDL) of a proton exchange membrane fuel cell (PEMFC) affects the transfer of the reaction gas and the water flooding phenomenon. First, the three-dimensional numerical model of the GDL was reconstructed by the stochastic reconstruction method, and the kinetic behaviors of liquid water in the conventional GDL, circular groove GDL, and elliptical groove GDL were compared and analyzed, based on which the liquid water penetration time, the effective diffusion rate of oxygen, and relative permeability of water in the three GDLs were analyzed, and the results of the study found that the circular groove GDL had the best drainage effect. Second, based on the PEMFC with serpentine channels, an electrochemical model of the GDL with circular grooves was arranged in the flow field, and the effects of the groove depth distribution and center spacing of circular grooves on its performance were numerically investigated. It was found that the presence of circular grooves enhanced the transfer rate of reactants from the GDL to the catalytic layer and increased the current density. Oxygen concentration uniformity and under-rib convection were enhanced when the groove depth was designed to have a power function distribution with an exponent close to 1, effectively reducing flooding. The best drainage effect was achieved when the groove spacing was 2 mm, and also the cell performance was more stable.