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Inorganic nanopores occurring in the shale matrix have strong hydrophilicity and irreducible water (IW) film can be formed on the inner surface of the pores making gas flow mechanisms in the pores more complex. In this paper, the existence of irreducible water (IW) in inorganic pores is considered, and, based on the Knudsen number (<i>K</i><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mi>n</mi></msub></semantics></math></inline-formula>) correction in shale pores, a shale gas apparent permeability model of inorganic nano-pores is established. The effect of the <i>K</i><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mi>n</mi></msub></semantics></math></inline-formula> correction on the apparent permeability, the ratio of flow with pore radius and the effect of IW on the apparent permeability are assessed. The main conclusions are as follows: (1) at low pressure (less than 10 MPa) and for medium pore size (pore radius range of 10 nm–60 nm), the effect of the <i>K</i><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mi>n</mi></msub></semantics></math></inline-formula> correction should be considered; (2) considering the effect of the <i>K</i><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mi>n</mi></msub></semantics></math></inline-formula> correction, bulk phase transport replaces surface diffusion more slowly; considering the existence of IW, bulk phase transport replaces surface diffusion more slowly; (3) with increase in pressure, the IW effect on gas apparent permeability decreases. Under low pressure, the IW, where pore size is small, promotes fluid flow, while the IW in the large pores hinders fluid flow. In conditions of ultra-high pressure, the IW promotes gas flow.