In terms of freezing process of liquid water inside gas diffusion layer for proton exchange membrane fuel cell(PEMFC) under pore-scale prospective, a mesoscopic simulation tool is proposed here to be involved in PEMFC-lattice Boltzmann method(LBM). First, true gas diffusion layer structure for PEMFC was built in pore-scale level. Then, accuracy of thermophysical parameters in the model was validated through one-dimensional half-space solidification, two-dimensional solidification in semi-infinite corner and two-dimensional solidification in cavity with porous numerical experiments, proving the effectiveness of application of lattice Boltzmann method on freezing mechanism in gas diffusion layer for PEMFC. Finally, the freezing process of gas diffusion layer with porosity ranging from 0.5 to 0.9 in pore-scale was investigated. The simulation results show that for two-dimensional gas diffusion layer with 0.5, 0.6, 0.7, 0.8 and 0.9 porosity, the dimensionless freezing time F0 is 2.67, 3.11, 3.68, 4.31 and 4.84, respectively and the dimensionless freezing time for cases with natural convection is 0, 0, 0.001, 0.001 and 0.007 less than that without natural convection, respectively.