CO2 storage in deep unrecoverable coal seams has become an effective method to curb greenhouse gas emission, which also contributes to an increase in coalbed methane (CBM) production. Due to high temperature and pressure in deep coal seams, the injected CO2 remains in a supercritical state. However, the influence of injecting supercritical CO2 into coal seams on coal permeability is not particularly clear at present. Therefore, this paper conducted a series of studies through high-pressure triaxial setups on the naturally fractured coal, the coal adsorbing supercritical CO2 for different times, and supercritical CO2-treated coal, respectively. In the experiment, the laws of coal permeability variation with different adsorption times of supercritical CO2 under different gas injection pressure were first determined. Results indicate that there is a decline in coal permeability in the initial stage because of the great swelling deformation induced by adsorption. Besides, the coal may find a rebound in permeability in the later phase if its mechanical properties have been changed after repeated adsorption. Meanwhile, He was applied to measuring the permeability of original coal and the coal completely desorbing supercritical CO2, respectively. On the basis of a comparison between their permeability values, the latter has higher permeability. It directly indicates that supercritical CO2 has extraction and dissolution effects on organic matter and inorganic minerals in coal, respectively, thus enhancing the permeability. To further support this point of view, pore characteristics of such two kinds of coal were determined through mercury intrusion method. It is demonstrated that the supercritical CO2-treated coal has well developed and connected pore system, with a rise in the proportion of meso- and macro-pores as well as total pore volume. In addition, the coal with different adsorption times varies in permeability evolution laws under the same effective stress. Inspired by such variation, this paper proposed a new gas injection method, that is, injection pressure rose gradually after cyclic adsorption of supercritical CO2, which provides a certain reference for efficient gas injection.