The flow and freezing process of liquid water in the gas diffusion layer (GDL) is studied using a proposed lattice Boltzmann method that integrates the multi-component pseudo-potential model and the enthalpy-based method. The evolution of liquid water, ice, and temperature distributions inside the GDL during this process is specifically analyzed, and the effect of GDL porous structure, such as porosity and carbon fiber diameter, is discussed. Results indicate that liquid water exhibits a propensity to break through the GDL through the regions characterized by larger pores, subsequently forming a liquid droplet on the GDL surface and beginning to freeze. The freezing process extends from the droplets to the CL side through the liquid pathways within the GDL. In addition, liquid water is more prone to freezing around carbon fibers. Due to the released latent heat during freezing, the temperature at the liquid water/ice interface stabilizes at 273 K. Moreover, it is also demonstrated that a large porosity and coarse carbon fibers both facilitate the flow of liquid water into the GDL where it then freezes, leading to more serious blockage of pores by ice and liquid water.