This work presents a new method to reconstruct the microstructure of carbon fiber gas diffusion layer (GDL), which is used to study the effect of velocity field in rough channels on GDL seepage. The random distribution model of pore channels in the diffusion layer is obtained by using the rough element and fractal theory. By distinguishing the hydrophilicity/hydrophobicity of the channel wall, four parameters, namely, the dispersion velocity ratio, the slip enhancement coefficient, the viscosity enhancement coefficient, and the microscale effect enhancement coefficient, are obtained. With accurate internal velocity distribution reconstructed as a control factor, and the effective seepage coefficient model is obtained by combining Darcy's law. The flow process of liquid water in GDL duct is simulated, and the influence of different roughness and contact angle on liquid water transmission performance is analyzed. The results show that the distributions of dispersion velocity, viscosity and slip velocity in the diffusion layer are affected by the random distribution of channel roughness elements and the non-uniform fluid solid interaction, and the four control factors act together on the flow process of liquid water and promote the discharge of liquid water. Under the same roughness, when the contact angle is 0o~180o, the promotion of hydrophilic wall slip effect conteracting the inhibition of dispersion effect and viscosity increases, and the promotion of hydrophobic wall slip effect conteracting the inhibition of dispersion effect and viscosity decreases, and the slope of flow change curve increases significantly at first and then decreases gradually. The newly established effective seepage coefficient model of liquid water in the diffusion layer can accurately describe the flow law in GDL, which has certain guiding significance for the internal water management of GDL.