An approach to predict the gas permeability of membrane polymers after supercritical CO2 treatment is proposed. The approach is based on the connection of the temperatures of secondary relaxation transitions with the effective sizes of mobile free volume elements in the polymers. The correlation between permeability of nitrogen and effective sizes of mobile holes for a set of polymers is established. The effect of supercritical CO2 on the nitrogen permeability of polycarbonate, polysulfone, polyvinylbutyral is analyzed by FTIR spectroscopy of low-molecular weight conformationally-inhomogeneous compounds introduced in the polymers. Membranes were exposed at 40 MPa and 333 K for 4 h through static treatment and dynamic treatment separately. For polyvinylbutyral, the nitrogen permeability did not change after supercritical CO2 modification while for polysulphone, the effective volume of mobile holes increased, but the nitrogen permeability decreased. For polycarbonate after supercritical CO2, the effective volume of mobile holes and the nitrogen permeability increased.