A microporous layer (MPL) is a transition layer with a porous material structure, located between the gas diffusion layer (GDL) and catalyst layer (CL) in a proton exchange membrane fuel cell (PEMFC). It not only significantly improves electron transfer and heat conduction in membrane electrode assembly, but also effectively manages liquid water transport to enhance the fuel cell performance. The MPL is usually coated on one side of the GDL. The fragile nature of MPL makes it challenging to characterize the effective transport properties using experimental methods. In this study, a stochastic numerical method is implemented to reconstruct the three-dimensional microstructure of an MPL consisting of carbon particles and PTFE. The reliability of the MPL reconstructed model is validated using experimental data. The relationship between the effective transport properties and the compression strain is obtained using the Pore Scale Model (PSM), while the relationship between the liquid water saturation and capillary pressure is solved by Lattice Boltzmann Method (LBM). The effective transport properties in the MPL are then imported into the two-phase flow fuel cell model. It is found that the effective transport parameters in MPL obtained by PSM and LBM can improve the accuracy of the model calculation. This study provides an effective method to reconstruct the microstructure of MPL that can generate precise MPL transport parameters for utilization in various PEMFC performance prediction models.