An optimized simulated annealing algorithm was used for the reconstruction three-dimensional pore structure of carbon fiber/polyvinyl alcohol fiber composite paper (CP). The effect of carbon fiber length, carbon fiber percentage, and dispersant amount on the pore structure of CP were first investigated. Then, the seepage simulations were performed leveraging the reconstructed equivalent pore network model for different CP samples. Furthermore, the impact of microscopic pore structure characteristics, including throat radius, coordination number, and pore-throat ratio, on the relative permeability of gas and water phases were quantified. An increase in the length and percentage of carbon fiber resulted in the pores and throats number decreasing, but increasing the average radius of pores and throats. Both throat radius and coordination number demonstrated a positive correlation with the relative permeability of gas and water phase. In contrast, the pore-throat ratio exhibited an inverse relationship with the relative permeability of gas phase, while showcasing a positive association with the relative permeability of water phase. This study provides an important reference for determining the microporous structure of CP and investigating the seepage mechanism.