The gas diffusion layer (GDL), a core component of the proton exchange membrane fuel cell (PEMFC), is integral to thermoelectric and gas-liquid transport. Recognizing the impact of mechanical compression on transport properties and cell performance, it is crucial to comprehensively study the GDL's effect on effective transport performance. In this study, two types of GDLs, Toray GDL fabricated by wet-laid and Freudenberg GDL fabricated by dry-laid, are first reconstructed. Then, their stress-strain distributions under various mechanical compression ratios from 0 to 40 % are simulated using the finite element method, along with the effects of mechanical pressures on the microstructural parameters. Finally, a pore scale model is utilized to obtain the effective transport properties of the two types of GDLs under ten different compression ratios. The results show that Freudenberg GDL exhibits a more rapid stress transfer with a more uniformly distributed stress, while Toray GDL displays a slower stress transfer with a more differentially distributed stress. Notably, the pore size decreases significantly by approximately 60 % in both GDL types when the compression ratio increases from 0 % to 40 %. As the mechanical compression ratios increases from 0 to 40 %, the tortuosity of Toray GDL and Freudenberg GDL in the in-plane/through-plane direction increases by 78 %/50 % and 81 %/86 %, respectively. The conductivity of Toray GDL and Freudenberg GDL increases by 150 %/650 % and 130 %/140 % in the in-plane/through-plane direction, respectively, when the compression ratio is increased to 40 %. Additionally, a 20 % compression ratio is identified as an optimal point for both GDLs to balance gas diffusion and thermoelectric conduction.