Coal permeability is related to the fracture-pore structure of coal and is a key factor in determining gas drainage efficiency. The characteristics of the methane flow in coal fractures are different from those in coal matrix pores. However, due to the difficulty of observing fast methane flow in coal fractures, the effect of gas flow in coal fractures on coal permeability has seldom been considered and investigated. In this study, a cylindrical coal sample is used for the measurement of coal permeability under different gas pressures, and an abrupt change in coal permeability evolution was observed. Then, a tandem fracture-pore permeability model was adopted to analyze these new methane flow phenomena. In this permeability model, the deformation of coal fractures was directly analyzed and modeled without the reversed derivation. With the consideration of elastic modulus of coal fractures, the deformation of coal fractures is controlled by the effective strain of coal fractures, the adsorption-induced strain and effective strain of coal matrix. The research results show that (1) coal fractures quickly and significantly influence coal permeability by resisting coal deformation; (2) a complete evolution of coal permeability consists of the fast permeability change caused by methane flow in coal fractures and the slow permeability change caused by methane flow in coal matrix; (3) the low efficiency of gas mass exchange between coal fractures and coal matrix leads to a two-stage evolution for gas desorption flow and coal permeability.