The deformation of gas diffusion layer (GDL) under compacting pressure has a close relationship with transport properties, and electrical and thermal conductivity of proton exchange membrane fuel cell (PEMFC). In this paper, two kinds of GDL material models with different material parameters are studied with the finite element method (FEM). Taguchi orthogonal experiments and analysis of variance (ANOVA) are performed to determine their effects on mechanical analysis of GDL deformation in PEMFC. Finally, the effects of material parameters on GDL diffusion and electrical performance are discussed. The results reveal that elastic modulus (E) is the only factor affecting the maximum displacement for GDL with isotropic model when the Poisson's ratio (ν) is in the range of 0–0.1. For orthotropic model, the through‐plane elastic modulus (Ez) has a great impact on both the deformation and contact pressure. In‐plane elastic modulus (Ex) and through‐plane shear modulus (Gxz) have significant influences on contact pressure. Ez has a great impact on diffusion and electrical performance of GDL, while the effects of Ex, Gxz and ν are negligible. In addition, orthotropic GDL material model and the parameters utilized are effective in analyzing the deformation of GDL.