The gas diffusion layer (GDL) is an important component of the proton exchange membrane fuel cell (PEMFC) and is critical to water management in fuel cells. This paper combines the random reconstruction model with the volume of fluid (VOF) method to numerically simulate liquid water transport in the GDL. The GDL with realistic porosity and pore size distribution is constructed based on Toray060 carbon paper. The VOF method is then used to simulate the process of liquid water imbibition. Unlike previous studies that focused solely on contact angle while neglecting the morphological structures such as polytetrafluoroethylene (PTFE) content and porosity, this article investigates the effects of different contact angles, PTFE content, and porosity on water transport in the GDL. A sensitivity analysis of the three factors is performed using the Sobol method. The results show that the GDL without PTFE, with a porosity of 0.78 and a contact angle of 120 degrees, exhibits a water saturation level of 0.668 and a stable breakthrough time of 0.611 s. As the contact angle of the GDL increases, the carbon fibers exhibit a greater repelling force on the water, leading to more pronounced liquid water capillary fingering. This accelerates the process of liquid water finding a pathway, thereby reducing the breakthrough time and lowering the water saturation. In the sensitivity analysis, the impact of morphological structures such as PTFE content and porosity on water saturation and breakthrough time is less significant than that of the contact angle, but should not be ignored. This is because the morphology affects the overall water distribution through spatial structure. Although its influence is not as direct as capillary forces, it still imposes a significant constraint on water flow within the GDL. Additionally, the GDL with a porosity of 0.78, a contact angle of 130 degrees, and 20% PTFE demonstrates the best water management performance.