The effect of thickness in multilayer thin-film composite membranes on gas permeation has received little attention to date, and the gas permeances of the organic polymer membranes are believed to increase by membrane thinning. Moreover, the performance of defect-free layers with known gas permeability can be effectively described using the classical resistance in series models to predict both permeance and selectivity of the composite membrane. In this work, we have investigated the Pebax®-MH1657/PDMS double layer membrane as a selective/gutter layer combination that has the potential to achieve sufficient CO2/N2 selectivity and permeance for efficient CO2 and N2 separation. CO2 and N2 transport through membranes with different thicknesses of two layers has been investigated both experimentally and with the utilization of resistance in series models. Model prediction for permeance/selectivity corresponded perfectly with experimental data for the thicker membranes. Surprisingly, a significant decrease from model predictions was observed when the thickness of the polydimethylsiloxane (PDMS) (gutter layer) became relatively small (below 2 µm thickness). Material properties changed at low thicknesses—surface treatments and influence of porous support are discussed as possible reasons for observed deviations.