Flexible metal‐organic frameworks (MOFs) are promising candidates for adsorptive separations, but achieving a balance among flexibility, adsorption capacity, and selectivity remains challenging. Herein, we report a novel flexible MOF, Ni(bhdc)(ted)0.5 (ZUL‐C6), incorporating hybrid three‐dimensional alkane‐bridged ligands, which realizes high‐capacity molecular sieving for hexane isomer separation ‐ a critical process in the petroleum industry. The alkyl‐rich, confined pore system within the ZUL‐C6 framework facilitated a strong affinity for n‐hexane and 3‐methylpentane. However, the narrow pore size and the constraint flexibility limited the uptake of 2,2‐dimethylbutane (< 4.0 mg/g), accompanied by a high gate‐opening pressure. The gating behavior was elucidated by guest‐loaded single‐crystal (SC) X‐ray diffraction and density functional theory (DFT) simulations, which revealed a unique SC to SC transformation driven by the non‐centrosymmetric rotation of the 3D bhdc linker and distortion of the metal cluster and pillar units, along with a high deformation energy barrier. As a result, ZUL‐C6 exhibited not only significantly higher uptake and selectivity than the industrially used 5A molecular sieve, but also the record‐high nHEX/3MP breakthrough uptake (92.8/73.9 mg/g) and unprecedented 22DMB producing time (309.2 min/g, corresponding to the productivity of 770 mmol/kg and yield of 92.8%) among reported MOFs.