This paper presents a continuum-scale diffusion-based model informed by pore-scale data for gas transport in organic nanoporous media. A mass transfer and adsorption model is developed by considering multiple transport and storage mechanisms, including bulk diffusion and Knudsen diffusion for free phase, surface diffusion for sorbed phase, and multilayer adsorption. The continuum-scale diffusion-based governing equation is developed solely based on free phase concentration for the overall mass conservation of free and sorbed phases, carrying a newly-defined effective diffusion coefficient and a capacity factor to account for multilayer adsorption. Diffusion of free and sorbed phases is coupled through the pore-scale simplified local density method based on the modified Peng-Robinson equation of state for confinement effects. The model is first utilized to analyze pore-scale adsorption data from the krypton (Kr) gas adsorption experiment on graphite. Then we implement the model to conduct sensitivity analysis for the effects of pore size on gas transport for Kr-graphite and methane-coal systems. The model is finally used to study Kr diffusion profiles through a coal matrix obtained through X-ray micro-CT imaging. The results show that the sorbed phase occupies most of the pore space in organic nanoporous media due to multilayer adsorption, and surface diffusion contributes significantly to the total mass flux. Therefore, neglecting the volume of sorbed phase and surface diffusion in organic nanoporous rocks may result in considerable errors. Furthermore, the results reveal that implementing a Langmuir-based model may be erroneous for an organic-rich reservoir with nanopores during the early depletion period when the reservoir pressure is high.