The mass transport and electrochemical reaction in the catalyst layer (CL) have a great impact on the performance of proton exchange membrane fuel cells (PEMFCs). In this study, a random algorithm is used to reconstruct the microstructure of the CL. The lattice Boltzmann method (LBM) is used to simulate the mass transport and electrochemical reaction in the CL. The CLs with ionomer/Pt gradient distribution are designed and then compared in terms of the oxygen concentration distribution, the number of reaction site and the reaction rate. The gradient type and number of gradient layers are also studied. It is found that the oxygen diffusion process and electrochemical reaction rate are significantly affected by the Pt/ionomer distribution. Compared with the uniform distribution CL, the reaction rate of CLs with ionomer/Pt gradient distribution can be improved by 14.4 % and 22.2 %, respectively.