In this study, novel Pebax-derived ultra-microporous carbon molecular sieve composite membrane assisted by polydopamine (PDA) interlayer was synthesized by dip-coating and pyrolysis method. Pebax was first explored as the precursor and PDA was selected as flexible coating layer on the polymeric substrate in preparation of CMS composite membranes. Pebax had long linear chain polyamine structure and contained large number of carbonyl groups and hydrogen bonds that were pyrolyzed under relatively low temperature. Compared with incorporating inorganic interlayer, the PDA organic interlayer constructed under mild condition had excellent adhesion towards the polymeric support. Since the intrusion of precursor Pebax into the pore of substrate was prevented, the channels of passage were shortened and the transport of gas molecules was greatly promoted. Through designable chemical bonding resistant to harsh conditions, the adhesion between organic interlayer and CMS layer were kept strong due to natural compatibility of materials, leading to the formation of defect-free CMS membranes with enhanced stability in operation. The fabricated CMS membrane displayed excellent H2/CO2 selectivity of 40.69 and very competitive permeability of 1.23 × 10−7 mol m−2 Pa−1 s−1.