Gas transport in coal induces effective stress variation, matrix swelling/shrinkage, and significantly affects matrix and fracture deformation, resulting in porosity and permeability evolution. However, the heterogeneity and anisotropy of coal are neglected in dual porosity models, which can lead to the deviation from the real physical mechanisms. To uncover the permeability evolution, especially the influence of dynamic matrix-fracture interaction for real fracture distribution, advanced virtual simulation is proposed. In this study, real fracture geometry is taken into account in the physical model based on the CT-scan image, while the mathematical models for coal deformation and gas flow are established. Our calculations are verified against a long-term experimental data under the same boundary condition. Accordingly, the real matrix-fracture interaction caused by adsorption-induced matrix deformation has been visually exhibited, and some new insight into the behavior of fracture permeability in real materials is offered. The results indicate the non-uniform distribution of fracture geometry is responsible for the nonmonotonic change of permeability. It also found that injection pressure, Langmuir strain constant and initial matrix permeability have important influences on the fracture permeability evolution. This research provides valuable insight into the understanding of the permeability change for the real fracture spatial distribution in coal.