The gas diffusion layer (GDL) is a key component to realize effective gas transport in the electrode of proton exchange membrane fuel cells. To study the effect of different structural parameters on the mass transfer characteristics of the GDL, a developed random reconstruction algorithm is proposed to generate three-dimensional (3D) GDLs with different structures, and the lattice Boltzmann method is used to simulate the flow behavior of reactant gases in the GDL. Through the calculation of the tortuosity and the comparison with the results reported in the references, the accuracy of the model in this paper is demonstrated. The outlet velocity and average velocity of the gas, the gas phase tortuosity, and diffusivity of the GDL are calculated by changing the structural parameters of carbon fiber diameter, porosity, and thickness. It is found that increasing the diameter of the carbon fiber from 7 to 9 mu m can increase the reactant gas velocity but has little effect on the improvement of GDL diffusion characteristics. Increasing the porosity from 60 to 80% can significantly increase the reactant gas velocity and improve the diffusion characteristics of the GDL. Increasing the thickness from 112 to 280 mu m, the reactant gas velocity is significantly reduced, and the diffusion characteristics of the GDL are weakened, but the change is not obvious. Finally, the influence of GDL structural parameters on electrical conductivity is discussed.