This study employed Micro X-ray computed tomography (Micro-CT) to reconstruct the gas diffusion layer (GDL) in proton exchange membrane fuel cells (PEMFCs) and used lattice Boltzmann method (LBM) simulations to investigate the dynamic behavior of liquid water in the multiscale space of the GDL and gas channel (GC). The results showed that the transport of liquid water from GDL to GC through the interface of GDL-land and GDL-GC were divided into four stages: large pore filling, through-plane breakthrough, in-plane diffusion, and rapid transport into GC. The wettability of GC wall and GDL affects the transport and distribution of liquid water. When the contact angle on the GC wall was less than 90°, it promoted liquid water transport to the top GC wall, resulting in faster internal flow formation. Conversely, contact angles exceeding 90° caused liquid water to break through the GDL-GC interface from pores away from the GC wall. When the contact angle of the GDL was in the range of 110°–150°, both excessively large and excessively small contact angles hindered water transport and management. Maintaining the contact angle of the GDL around 130° enhanced the breakthrough path and transport speed of liquid water into the GC, and it also reduces localized liquid water accumulation.