To strengthen interfacial adhesion between selective carbon molecular sieve (CMS) layers and α-Al2O3 substrates, mordenite framework inverted (MFI)-type intermediate layers were synthesized to reduce pore sizes and improve chemical characteristics of underlying substrates and consequently facilitate formation of CMS layers. MFI-type zeolite intermediate layers were prepared on α-Al2O3 substrates via secondary growth of seeds to form polycrystalline zeolite layers with a-oriented crystallites. These crystallites increased cross-link strength between separation layers as well as gas pair separation performance. When a porous substrate was treated with silica seeds and covered with an MFI intermediate layer, CMS selectivity for H2/CH4 increased to 260.9 with permeability towards H2 of 2224Barrer. These modifications improved the mechanical stability of CMS layers and will assist in their commercialization.