Chemical vapor deposition (CVD) with methyldiethoxysilane (MDES) for MFI zeolitic pore size reduction is an effective way to improve the H-2/CO2 separation factor of zeolite membranes. However, only good membranes with few intercrystalline defects are able to show considerable improvement in H-2/CO2 separation factor through CVD modification. It is unreliable to evaluate the membrane quality on the basis of the H-2/SF6 or N-2/SF6 ideal separation factor because the SF6 adsorption-induced crystal swelling causes shrinkage of the intererystalline defects in the MFI zeolite membranes. In this study, the quality of MFI zeolite membranes was evaluated on the basis of their performance in separating equimolar H-2/CO2 mixture gas at room temperature. High-quality membranes are more selective to CO2 molecules rather than H-2 at room temperature due to the adsorption of CO2 into the zeolitic pores and blocking of the pore channels for H-2 diffusion. The effectiveness of the quality evaluation method was confirmed by on-stream CVD modification of MFI zeolite membranes with different initial H-2/CO2 separation factors/ideal separation factors at room temperature. Experimental results showed that only those membranes with low H-2/CO2 separation factor at room temperature (good membranes) showed improvement in H-2/CO2 separation factor through CVD modification. For the CVD modified zeolite membrane with good initial quality, the permeance of H-2 is lower than that of He with an activated diffusion behavior for small gas molecules in the modified zeolitie pores.