The gas diffusion layer (GDL) is a crucial component of Proton Exchange Membrane Fuel Cells (PEMFC), water flooding will occur during the operation of PEMFC, resulting in performance degradation, and its water management plays a significant role in PEMFC performance. To investigate the transport mechanism of liquid water in GDL, the lattice Boltzmann method to simulate the behavior of GDL droplets using the 'random reconstruction' method. The accuracy of this model by calculating the tortuosity and comparing it with reported results in literature. The effects of different GDL structural parameters on permeability were studied. Finally, the conductivity and thermal conductivity of the GDL in various directions were examined. The results indicate that the porosity error of the three-dimensional structure model of GDL is within 0.01, enabling a realistic simulation of the GDL structure. The average error between the calculated results and the Bruggeman equation is only 2.5362%, and the average error compared to the reference results is less than 6%, demonstrating the model's high accuracy. As the porosity and fiber diameter of the GDL three-dimensional structure model increase, the permeability also increases. Conversely, the permeability decreases with an increase in the thickness of the GDL three-dimensional structure model. Moreover, an increase in GDL porosity leads to a gradual decrease in electrical conductivity and thermal conductivity in both the thickness and plane directions, with a more pronounced effect on the thickness. This study uncovers the transport characteristics of liquid water in the gas diffusion layer, which can inform the optimization of GDL structure design and serve as a theoretical reference for enhancing water management in proton exchange membrane fuel cells. Future research directions will focus on further optimizing the three-dimensional structure of GDL to improve its transmission characteristics and overall performance.