During the assembly process of proton exchange membrane fuel cell (PEMFC) stacks, the gas diffusion layer (GDL) will deform due to the assembly pressure and invade the flow channel. Utilizing the volume of fluid (VOF) method, numerical models were established for flow channel with rectangular, trapezoidal, and square cross-sections to investigate the two-phase gas-liquid flow behavior under varying degrees of GDL intrusion. The insights into liquid retention, drainage effectiveness, and GDL surface mass transfer area were analyzed. In instances of GDL intrusion into flow channel, the fragmentation of liquid during the discharge process decreases, facilitating the accumulation of liquid into larger droplets or film formation. The intrusion of GDL into the flow channel affects the liquid retention during the internal drainage process, with rectangular cross-section channel exhibiting longer drainage time, and trapezoidal and square cross-section channel experiencing delayed liquid discharge moments. In the presence of GDL intrusion into flow channel, the reduction in channel cross-sectional area results in an increased inlet gas velocity, maintaining a stable discharge velocity for relatively clustered liquid droplets without a substantial decrease. For cases of substantial GDL intrusion, the rectangular cross-section channel shows a higher incidence of liquid droplets adhering to the channel sidewalls and GDL surface, resulting in a larger GDL surface coverage. Additionally, in channels with significant GDL intrusion, the trapezoidal cross-section channel exhibits the formation of a stable film flow at the top, with higher drainage velocity and smaller GDL surface coverage.