To establish a permeability prediction model applicable to deep coal seam gas drainage engineering and accurately describe the fracture structure characteristics of fractured coal rock bodies and assess the impact of different fracture parameters on gas permeability characteristics, three-dimensional (3D) reconstruction and quantitative characterization of the fracture surfaces were performed. Permeability tests and numerical simulations were conducted on fractured coal-rock bodies with varying fracture dip angles and connectivity under different confining pressures. The numerical simulation results further revealed the gas flow patterns and distribution characteristics within coal rock masses containing different fracture dip angles and connectivities under varying confining pressures. These simulations validated and supplemented the experimental findings. The results indicate the permeability of the coal-rock body decreases with an increase in fracture dip angle. A localized diffusion zone forms within the coal-rock matrix near the fracture channel, and the size of this zone decreases as the fracture dip angle increases. In the gas exchange areas between fractures of different connectivity, there are phenomena of intersecting and biased flow. Near these gas exchange areas, there is also an increase in local permeability velocity within the coal-rock matrix. During the confining pressure loading stage, the permeability of specimens containing coal-rock bodies with different fracture dip angles and connectivity decreases with increasing confining pressure. During the confining pressure unloading stage, the permeability of the specimens increases but remains lower than the permeability measured at the same confining pressure during the loading stage. Fracture dip angle and connectivity are the primary factors influencing the permeability capacity of coal-rock bodies, particularly at low confining pressure levels. Fracture roughness significantly affects permeability. The rougher the fracture, the greater the dispersion of gas permeability velocity distribution within the fracture. Fracture roughness exerts a “retarding” effect on gas flow, and this effect becomes more pronounced with increasing fracture roughness. This research revealed the regulatory mechanism of fracture evolution on gas migration under engineering disturbances.