Gas transport in nanoporous media is fundamentally governed by confinement effects and surface roughness, which challenge the applicability of conventional continuum theories. In this study, a molecular-based apparent permeability model for nanoporous flows is established by incorporating confinement effects, surface roughness, and wettability using a bottom-up approach. The roughness effect is incorporated through a correction function calibrated from molecular simulations, which characterizes the suppression of slip behavior induced by surface roughness. A generalized hydrodynamic model is employed to describe pore-scale transport behavior in smooth nanochannels, from which a semi-empirical scaling law for slip length is developed as a function of fluid-solid interactions, pore size, finite molecular size, and Knudsen number. The resulting slip-length scaling law is then incorporated into a slip-corrected permeability relation to obtain the apparent permeability model for rough nanoporous media. The new model is validated through systematic comparisons with molecular simulation results, experimental data, and existing theoretical models, demonstrating its capability to accurately capture nanoscale transport behavior under varying surface roughness conditions. Parametric analyses further show that the apparent permeability increases with hydrophobicity while decreases with surface roughness, both of which have been largely overlooked in previous apparent permeability models. Overall, the proposed model provides a physically grounded framework linking molecular-scale interactions with fluid transport in nanoporous media.

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• Flow confinement
• Flows in porous media
• Roughness
• Transport phenomena
• Nonequilibrium systems