Isoporous nanomaterials, with their proven potential for accurate molecular sieving, are of substantial interest in propelling sustainable membrane techniques. Covalent organic frameworks (COFs) are prominent due to their customizable isopores and chemistry. Still, the discrepancy in experimental and theoretical structures poses a challenge to developing COF membranes for molecular separations. Here, we report high‐selectivity sieving of complex ultrafine molecules through solvating pore‐to‐pore‐aligned two‐dimensional COF membranes. Our structurally oriented membrane shows reversible interlayer expansion with intralayer shift in response to solvent exposure. This dynamic deformation induced by solvents leads to a reduction in the aperture of the membrane’s sieving pores, which correlates with the number of COF layers. The resultant membranes yield largely improved molecular selectivity to discriminate binary and trinary complex mixtures, exceeding the conventional COF membranes. The membrane’s robustness against solvents and physical aging permits extremely stable microporosity and reliable operation for over 3000 h. This exceptional performance positions our membrane as an alternative to enriching and purifying value‐added chemicals, such as active pharmaceutical ingredients.
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