Coal deformation is one of the leading problems for carbon dioxide (CO2) sequestration in coal seams especially with respect to different-phase CO2 injection. In this paper, a series of core flooding tests were conducted under different confining stresses (8–20 MPa), injection pressures (1–15 MPa), and downstream pressures (0.1–10 MPa) at 50 °C temperature to investigate the effects of coal deformation induced by adsorption and effective stress on sub-critical, super-critical, and mixed-phase CO2 permeability. Due to the linear relationship between the mean flow rate and the pressure gradient, Darcy Law was applied on different-phase CO2 flow. Experimental results indicate that: (1) Under the same effective stress, sub-critical CO2 permeability > mixed-phase CO2 permeability > super-critical CO2 permeability. (2) For sub-critical CO2 flow, the initial volumetric strain is mainly attributed to adsorption-induced swelling. A temporary drop in permeability was observed. (3) For super-critical CO2 flow, when the injection pressure is over 10 MPa, effective-stress-generated deformation is dominant over the adsorption-induced strain and mainly contributes to the volumetric strain change. Thus, there is a linear increase of the volumetric strain with mean pore pressure and super-critical CO2 permeability increased with volumetric strain. (4) For mixed-phase CO2 flow, coupling effects of adsorption-induced swelling and effective stress on the volumetric strain were observed but effective stress made more of a contribution. CO2 permeability consistently increased with the volumetric strain. This paper reveals the swelling mechanism of different-phase CO2 injections and its effect on coal permeability.