Mining operations produce a multiscale network of fractures in the coal seams. Permeability evolution in rocks is important for coal bed methane (CBM) and shale gas exploitation as well as for greenhouse gas storage. Therefore, this work presents laboratory tests and a coupled model using PFC3D and FLAC3D to simulate the stress induced permeability evolution in coal samples. Basic mechanical properties are determined via lab testing. The spatial distributions of different components inside the reconstructed samples produce a significant heterogeneity based on CT technique. A newly developed experimental system is employed to perform 3-dimensional loading and to measure the flow rate simultaneously. The evolution process is described by 5 distinct phases in terms of permeability and deformation. Triaxial tests are simulated with PFC3D using a novel flexible wall boundary method. Gas seepage simulations are performed with FLAC3D. Relations between hydraulic properties and fracture data are established. Permeability and volumetric strain show good nonlinear exponential relation after a newly introduced expansion point. Piecewise relations fit the whole process, the expansion point can be treated as critical point. The structural characteristics of the samples influence this relation before and after the expansion point significantly.