Understanding the long-term evolution of coal permeability under the influence of gas adsorption-induced multiple processes is crucial for the efficient sequestration of CO2, coalbed methane extraction and enhanced coal bed methane recovery. In previous studies, coal permeability is normally measured as a function of gas pressure under the conditions of constant effective stresses, uniaxial strains and constant confining pressures. In all these experiments, an equilibrium state between coal matrix and fracture is normally assumed. This assumption has essentially excluded the effect of matrix–fracture interactions on the evolution of coal permeability. In this study, we hypothesize that the current equilibrium assumption is responsible for the discrepancy between theoretical expectations and experimental measurements. Under this hypothesis, the evolution of coal permeability is determined by the effective stress gap between coal matrix and fracture. This hypothesis is tested through an experiment of CO2 injection into a coal core under the constant effective stress. In this experiment, the effective stress in the fracture system is unchanged while the effective stress in the matrix evolves as a function of time. In the experiment, the coal permeability was measured continuously throughout the whole period of the experiment (~ 80 days). The experimental results show that the core expands rapidly at the beginning due to the gas injection-induced poroelastic effect. After the injection, the core length remains almost unchanged. But, the measured permeability declines from 60 to 0.48 μD for the first month. It rebounds slowly for the subsequent 2 months. These results indicate that the effective stress gap has a significant impact on the evolution of coal permeability. The switch of permeability from the initial reduction (the first 30 days) to rebound (the subsequent 50 days) suggests a transition of matrix deformation from nearby the fracture wall to further away area. These findings demonstrate that the evolution of coal permeability is primarily controlled by the spatial transformation of effective stresses between matrix and fracture.