Discrimination of physically similar molecules by porous solids represents an important yet challenging task in industrially relevant chemical separations. Precisely controlled pore dimension and/or tailored pore surface functionality are crucial to achieve high‐efficiency separation. Metal‐organic frameworks (MOFs) are promising candidates for these challenging separations in light of their structural diversity as well as highly adjustable pore dimension/functionality. We report here a microporous, ftw‐type Zr‐based MOF structure, HIAM‐410 (HIAM=Hoffmann Institute of Advanced Materials), built on hexanuclear Zr6 cluster and pyrene‐1,3,6,8‐tetracarboxylate (ptc4−). Its crystallographic structure has been determined using continuous rotation electron diffraction (cRED) technique combined with Rietveld refinement against powder X‐ray diffraction data, aided by low‐dose high‐resolution transmission electron microscopy (HRTEM) imaging. The compound features exceptional framework stability that is comparable to the prototype MOF UiO‐66. Interestingly, the linker vacancies in the pristine MOF structure could be partially restored by post‐synthetic linker insertion. Its separation capability of hexane isomers is enhanced substantially upon the linker vacancy engineering. The restored structure exhibits efficient splitting of monobranched and dibranched hexane isomers at both room temperature and industrially relevant temperature. A highly robust ftw‐type zirconium‐based metal–organic framework has been constructed. Its linker vacancy sites are restored by post‐synthetic linker insertion, which notably enhances its separation performance toward alkane isomers.