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Predicting apparent gas permeability (AGP) in nanopores is a major challenge for shale gas development. Considering the differences in the gas molecule-pore wall interactions in inorganic and organic nanopores, the gas transport mechanisms in shale remain unclear. In this paper, gas flow channels in shale, which are separated into inorganic pores and organic pores, are treated as nanotubes. Inorganic pores are assumed to be hydrophilic, and organic pores are assumed to be hydrophobic. In organic pores, multiple bulk free gas and surface adsorbed gas transport mechanisms are incorporated, while the bulk gas and water film are considered within inorganic pores. This paper presents a unified multiple transport mechanism model for both organic nanopores and inorganic nanopores. Unlike the earlier models, the presented models consider the absorption, stress dependence, real gas, and water storage effects on gas transport comprehensively for the entire flow regime. The results are validated with published data which is more in line with the real situation. The results show that (1) the AGP decreases gradually as the pore pressure decreases but that the decrease is sharp in small pores, (2) the AGP decreases dramatically when considering the real gas effect at 50 MPa in a 2 nm pore size, and (3) for a small pore size at the critical high-water saturation, AGP might increase suddenly as the flow regime changes from continuum flow to slip flow. The findings of this study can help for better understanding of the gas transport mechanisms for the entire flow regime in shale.