In order to study the influence of the diffusion layer structure on the conductivity, drainage and gas conduction of the fuel cell, COMSOL Multiphysics was used to simulate and analyze the proton exchange membrane fuel cell. The variation of porosity of diffusion layer along thickness gradient, the mass transfer process by cathode side and the performance of fuel cell were simulated. The results show that the diffusion layer with gradient structure can reduce the occurrence of cathode water flooding, and the battery performance of the diffusion layer with gradient porosity distribution is better than that of the diffusion layer with uniform porosity distribution. At the same average porosity, the larger the gradient structure of porosity is, the stronger the drainage capacity of cathode side is, and the less residual liquid water is.