Considering the complex pore structure and the diffusion from the matrix system to the fracture system, the single phase flow model of natural gas is established, and one new diffusion coefficient formula is given in the paper. Finally the flow mechanism from the matrix to the fracture and the shale gas flow characteristics affected by the diffusion are analyzed. The results show that: the Darcy flow rate is proportional to the pressure gradient and permeability; and the Darcy flow mainly influences the flow in high pressure, but the diffusion obviously influences the gas flow in low pressure, the proportion of the diffusion flow rate is larger. With the increase of formation pressure, the diffusion flow rate decreases significantly. The diffusion flow rate has nothing to do with the permeability.