The flow of shale gas in nano scale pores is affected by multiple physical phenomena. At present, the influence of multiple physical phenomena on the transport mechanism of gas in nano-pores is not clear, and a unified mathematical model to describe these multiple physical phenomena is still not available. In this paper, an apparent permeability model was established, after comprehensively considering three gas flow mechanisms in shale matrix organic pores, including viscous slippage Flow, Knudsen diffusion and surface diffusion of adsorbed gas, and real gas effect and confinement effect, and at the same time considering the effects of matrix shrinkage, stress sensitivity, adsorption layer thinning, confinement effect and real gas effect on pore radius. The contribution of three flow mechanisms to apparent permeability under different pore pressure and pore size is analyzed. The effects of adsorption layer thinning, stress sensitivity, matrix shrinkage effect, real gas effect and confinement effect on apparent permeability were also systematically analyzed. The results show that the apparent permeability first decreases and then increases with the decrease of pore pressure. With the decrease of pore pressure, matrix shrinkage, Knudsen diffusion, slippage effect and surface diffusion effect increase gradually. These four effects will not only make up for the permeability loss caused by stress sensitivity and adsorption layer, but also significantly increase the permeability. With the decrease of pore radius, the contribution of slippage flow decreases, and the contributions of Knudsen diffusion and surface diffusion increase gradually. With the decrease of pore radius and the increase of pore pressure, the influence of real gas effect and confinement effect on permeability increases significantly. Considering real gas and confinement effect, the apparent permeability of pores with radius of 5 nm is increased by 13.2%, and the apparent permeability of pores with radius of 1 nm is increased by 61.3%. The apparent permeability model obtained in this paper can provide a theoretical basis for more accurate measurement of permeability of shale matrix and accurate evaluation of productivity of shale gas horizontal wells.