The gas diffusion layer (GDL) typically consists of a thin layer of carbon fiber paper, carbon cloth or nonwoven and has numerous pores. The GDL plays an important role that determines the performance of the fuel cell. It is a medium through which hydrogen and oxygen are transferred and serves as a passage through which water, generated by the electrochemical reaction, is discharged. The GDL tissue undergoes a compressive loading during the stacking process. This leads to changes in fiber content, porosity and resin content due to compressive load, which affects the mechanical, chemical and electrical properties of the GDL and ultimately determines fuel cell performance. In this study, the geometry of a GDL was modeled according to the compression ratios (10%, 20%, 30%, 40% and 50%), which simulated the compression during the stacking process and predicted the equivalent properties according to the change of GDL carbon fiber content, matrix content and pore porosity, etc. The proposed method to predict the equivalent material properties can not only consider the stacking direction of the material during stack assembling process, but can also provide a manufacturing standard for fastening compressive load for GDL.