Gas permeability is a significant parameter influencing gas extraction and coal-gas outburst prediction in coal seams. To investigate the effects of coal damage and shear deformation on fracture permeability, a damage variable is introduced to reflect the failure state of coal damage. A constitutive model is established with the increment of volumetric strain. The evolution model of fracture permeability influenced by shear and compression is obtained, and Hurst coefficient is applied to represent the roughness of fracture surface. Based on the dual permeability media of matrix pore and fracture, a gas-solid coupling software named TOUGH2(CH4)-FLAC is built by the secondary development of the codes of TOUGH2 and a DLL file for FLAC3D. A case study is performed to investigate the influences of damage and shear dilation on gas flow in the process of uniaxial compression using the proposed model. Numerical results show that the accumulation and coalescence of damaged elements largely control the failure of coal, and the damage zone is the main factor resulting in the failure of coal. The location of permeability change is highly related to the damage zone. The fracture permeability can be increased by two orders of magnitude in most of damage zones. The variety of fracture permeability in the shear damage zone increases drastically with the increase of shear dilation. The proposed method provides a theoretical basis for the development of gas control.