Rational design of high-performance stable metal–organic framework (MOF) membranes is challenging, especially for the sustainable treatment of hypersaline waters to address critical global environmental issues. Herein, a molecular-level intra-crystalline defect strategy combined with a selective layer thinning protocol is proposed to fabricate robust ultrathin missing-linker UiO-66 (ML-UiO-66) membrane to enable fast water permeation. Besides almost complete salt rejection, high and stable water flux is achieved even under long-term pervaporation operation in hash environments, which effectively addresses challenging stability issues. Then, detailed structural characterizations are employed to identify the type, chemical functionality, and density of intra-crystalline missing-linker defects. Moreover, molecular dynamics simulations shed light on the positive atomistic role of these defects, which are responsible for substantially enhancing structural hydrophilicity and enlarging pore window, consequently allowing ultra-fast water transport via a lower-energy-barrier pathway across three-dimensional sub-nanochannels during pervaporation. Unlike common unfavorable defect effects, the present positive intra-crystalline defect engineering concept at the molecular level is expected to pave a promising way toward not only rational design of next-generation MOF membranes with enhanced permeation performance, but additional water treatment applications.