To describe the degradation of proton exchange membrane fuel cells (PEMFCs), empirical degradation models of different indexes of PEMFCs are established. Firstly, the simulation process and assumptions of PEMFC degradation are proposed. Secondly, the degradation simulation results including the performance and distribution indexes under the different degradation levels are conducted by AVL FIRE M. Finally, the empirical degradation models of performance and distribution indexes are established based on the above simulation results and experimental data. The results show that the relationship between the experimental and simulation results is established by the index of current density. The empirical degradation models of current density, average equilibrium potential on the cathode catalyst layer (CL), average membrane water content, average oxygen molar concentration on the cathode CL, and average hydrogen crossover flux are the linear function. The empirical degradation models of average exchange current density on the anode CL, average hydrogen molar concentration on the anode CL, and average oxygen crossover flux are the quadratic function. The empirical degradation model of average activation overpotential on the cathode CL is the quintic function.