Shale gas resources are widely distributed and abundant in China, which is an important field for strategic replacement and development of oil and gas resources. Shale gas reservoirs has adsorption gas, free gas. The structure of different scale media, such as organic pores, are difficult to describe. Therefore, flow behavior cannot be simulated by conventional method. In this paper, the micro-scale fluid migration in shale gas reservoirs was established in a single pore, which coupled surface diffusion, slip flow, and viscous flow. On this basis, the fractal scale relationship was applied to describe the distribution of pore radius, tortuosity, and surface roughness. Based on the comprehensive characterization of static structure characteristics of porous media, such as pore size distribution, pore shapes, tortuosity and surface roughness, and the dynamic pore size influenced by various stresses, the apparent porosity/permeability model of organic matter considering singlephase multi-migration mechanism was established. The gas migration in organic porous media was analyzed with the apparent porosity/permeability model. The results show that the small pores in organic matter are the main storage space of gas (more than 95% of the gas is stored in pores less than 10 nm), and the large pores are gas flow channel. At the same time, the apparent porosity/permeability model combined with conventional Darcy equation can be used to describe the single-phase gas flow in shale gas reservoirs.