Hierarchically porous materials containing sub-nm ultramicropores with molecular sieving abilities and microcavities with high gas diffusivity may realize energy-efficient membranes for gas separations. However, rationally designing and constructing such pores into large-area membranes enabling efficient H2 separations remains challenging. Here, we report the synthesis and utilization of hybrid carbon molecular sieve membranes with well-controlled nano- and micro-pores and single zinc atoms and clusters well-dispersed inside the nanopores via the carbonization of supramolecular mixed matrix materials containing amorphous and crystalline zeolitic imidazolate frameworks. Carbonization temperature is used to fine-tune pore sizes, achieving ultrahigh selectivity for H2/CO2 (130), H2/CH4 (2900), H2/N2 (880), and H2/C2H6 (7900) with stability against water vapor and physical aging during a continuous 120-h test.