Understanding mechanisms of gas transport in shale matrix pores is of great importance for more accurate production prediction of shale gas wells. Shale matrix is generally considered to be composed of organic matrix and inorganic matrix, and the gas transport mechanisms in different types of matrix pores are different. To date, most of the gas transport models assume that the gas transport channels in shale porous media are cylindrical capillaries or slits with uniform pore size, which ignore the effect of pore size distribution (PSD) on gas transport capacity. In addition, there are few transport models considering the presence of water in inorganic matrix, and the gas transport capacity will be overestimated ignoring this factor. Therefore, a real gas transport model for shale matrix pores is proposed so that the shale gas transport behavior can be analyzed more accurately. First, the nanopores in shale matrix is represented by cylindrical capillaries, and a logarithmic normal distribution function is utilized to characterize the PSD in shale organic and inorganic porous media. Then, the gas transport models are constructed for organic porous media and inorganic porous media, respectively. The total transport model can be obtained by coupling the two types of models. What is more, the influence of stress dependence and real gas effect are taken into account in the models. After that, the models are validated, which show that the proposed models fit well with published experimental data. Finally, the influence of multiple factors on gas transport capacity is analyzed, the results show that the total apparent permeability increases with the increase of total organic carbon (TOC) when the pressure is higher than 5 MPa, and it decreases with TOC as the pressure is lower than 5 MPa. The adsorption and desorption of gas in organic nanopores cannot be neglected, and its influence on slip flow is greater than that on Knudsen diffusion. The apparent permeability of inorganic nanopores decreases with relative humidity (water film thickness), and it decreases more rapidly when the relative humidity is higher than 0.5. The PSD has a great influence on shale gas transport capacity of porous media, especially for inorganic porous media.