A coupled diffusion model based on continuum thermodynamics is developed to quantitatively describe the transport properties of glassy thin films during physical aging. The coupled field equations are then embodied and applied to simulate the transport behaviors of O2 and CO2 within aging polymeric membranes to validate the model and demonstrate the coupling phenomenon, respectively. It is found that due to the introduction of the concentration gradient, the proposed direct calculating method on permeability can produce relatively better consistency with the experimental results for various film thicknesses. In addition, by assuming that the free volume induced by lattice contraction is renewed upon CO2 exposure, the experimental permeability of O2 within Matrimid® thin film after short-time exposure to CO2 is well reproduced in this work. Remarkably, with the help of the validated straightforward permeability calculation method and free volume recovery mechanism, the permeability behavior of CO2 is also well elucidated, with the results implying that the transport process of CO2 and the variation of free volume are strongly coupled.