Laboratory test of coal permeability is generally conducted under the condition of gas adsorption equilibrium, and the results contribute to an understanding of gas migration in the original coal seams. However, gas flow under the state of non-equilibrium, accompanied by gas adsorption and desorption, is more common in coalbed methane (CBM) recovery and geological sequestration sites. Therefore, research on gas migration under the non-equilibrium state has a greater significance with regard to CBM recovery and geological sequestration. However, most permeability models, in which only one gas pressure has been considered, cannot be used to study gas flow under the non-equilibrium state. In this study, a new mathematical model, which includes both fracture gas pressure and matrix gas pressure, and couples the gas flow with the coal deformation, has been developed and verified. With the developed model, the spatial and temporal evolution of gas flow field during gas adsorption and desorption phases has been explored. The results show that the gas pressures present nonlinear distributions in the coal core, and the matrix gas pressure is generally lower than the fracture gas pressure during adsorption, but higher than the fracture gas pressure during desorption. For gas flow during adsorption, the main factor controlling permeability varies at different points. At the initial time, the permeability is dominated by the effective stress, and at the later time, the permeability in the part close to the gas inlet is mainly controlled by the matrix swelling, whereas that in the part close to the gas outlet is still dominated by the effective stress. For gas flow during desorption, from the gas inlet to the gas outlet, the permeability deceases at the initial time, and when the time is greater than 10,000 s, it shows a decreasing and then an increasing trend. The reason is that at the initial time, the permeability is dominated by the increased effective stress caused by the sharp decrease of the fracture gas pressure. Later, desorption of the adsorbed gas results in matrix shrinkage, which further leads to an increase of the permeability.