Proton exchange nembrane fuel cells (PEMFCs) are highly promising energy devices for future transportation and distributed power stations. The electrochemical performance of PEMFCs assembled with gas diffusion layer (GDL) of different porosity gradient distributions has been analyzed using the lattice Boltzmann method. A single-phase multi-component lattice Boltzmann model employing the active approach was developed to investigate the reactive gas flow within the GDL. Two types of GDLs with the same porosity, namely multilayer porosity gradient GDLs and linear porosity gradient GDLs, were generated to investigate the effect of the porosity gradient of the GDL on the electrochemical performance of PEMFC. The results show that the two types of porosity gradient GDL improve oxygen starvation problems and enhance water management, and that the GDLs with smaller porosity gradients can increase the mean current density. This paper develops the study of pore-scale analysis of PEMFC performance and can provide guidance for the design of GDL structures.