Abstract Crystalline membranes, represented by the metal‐organic framework (MOF) with well‐defined angstrom‐sized apertures, have shown great potential for molecular separation. Nevertheless, it remains a challenge to separate small molecules with very similar molecular size differences due to angstrom‐scale defects during membrane formation. Herein, a stepwise assembling strategy is reported for constructing MOF membranes with intrinsic angstrom‐sized lattice aperture lattice to separate organic azeotropic mixtures separation. The membrane is synthesized by redesigning the metal source, which reduces the coordination reaction rate to avoid cluster‐missing defects. Then, extra ligands are introduced to overcome the coordination steric hindrance to heal the linker‐missing defects. Ultralow‐dose transmission electron microscopy is used to realize a direct observation of the angstrom‐scale defects. For separating the challenging methanol‐containing ester or ether azeotropic mixtures with molecular size difference as small as <1 Å, the angstrom‐scale defect‐free MOF membrane exhibits an outstanding flux of ≈3700 g·m −2 h −1 and separation factor of ≈247–524, far beyond the upper‐bound of state‐of‐the‐arts membranes. This study offers a feasible strategy for precisely constructing angstrom‐confined spaces for diverse applications (e.g., separation, catalysis, and storage).