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Summary Zr-carboxylate metal-organic frameworks (MOFs) are structurally robust materials, in part due to their strong coordination bonds. The regioselective Zr–O bond cleavage and formation between 3D architectures are thus challenging and are heretofore unexplored. In this work, by introducing highly flexible 18-crown-6-ether functionalities into a homochiral Zr-MOF, we report an unprecedented topology transition in which a 4,10-connected framework undergoes a rapid solid-state transition into a thermodynamically more stable 4,8-connected analog by a regioselective-linker-elimination under ambient conditions. The transition process was unambiguously unraveled by single-crystal and powder X-ray diffraction studies, and we proposed a possible transition mechanism based on various control experiments and theoretical calculations. The excellent chemical stability and substantially expanded porosity and pore apertures endowed the transformed chiral MOF with an exceptional capacity for the enantioadsorptive and solid-phase extractive separation of the racemic drug molecule of lansoprazole with 98% ee and 93% ee, respectively.