Gating molecular separation using artificial sub‐nanoporous molecular sieves is highly desirable in large‐scale chemical and energy processing, such as gas separation, hydrogen recovery, carbon dioxide capture, seawater desalination, etc. However, it has remained an insurmountable challenge to create such materials. Herein, a binary meso‐reconstruction strategy to develop biomimetic sub‐nanoporous engineered aerogel molecular sieves (NAMSs) with reversible nanogating channels is demonstrated, in which sub‐1 nm pores (≈7 Å) provide coupling size‐thermodynamic gated functions that enable molecule discrimination and trapping in a reversible manner. The NAMSs show polarity‐reversible adsorption in which adsorbate molecules are discriminated by each gate‐admission sponge‐fiber molecular sieve, facilitating size/interface synergistically induced selective separation of 1,3,5‐trimethyl benzene/ethylene glycol with high separation factor and fast adsorption rate. The nanogating aerogel molecular sieves with molecularly defined sub‐1 nm nanoporous architecture (≈7 Å), Murray's law hierarchical channels, ultrahigh surface area (686 m2 g−1), and robust self‐supporting characteristics define a new benchmark for both aerogels and molecular sieves, exhibiting great potential in diversified on‐demand molecular separations that are prevalent in chemical, energy, and environmental processes.