Adsorptive separation by porous solids provides an energy-efficient alternative for the purification of important chemical species compared to energy-intensive distillations. Particularly, the separation of linear hexane isomers from its branched counterparts is crucial to produce premium grade gasoline with high research octane number (RON). Herein, we report the synthesis of a new, flexible zinc-based metal-organic framework, [Zn₅(μ₃-OH)₂(adtb)₂(H₂O)₅·5 DMA] (Zn-adtb), constructed from a butterfly shaped carboxylate linker with underlying (4,8)-connected scu topology capable of separating the C6 isomers nHEX, 3MP, and 23DMB. The sorbate-sorbent interactions and separation mechanisms were investigated and analyzed through in situ FTIR, solid state NMR measurements and computational modeling. These studies reveal that Zn-adtb discriminates the nHEX/3MP isomer pair through a kinetic separation mechanism and the nHEX/23DMB isomer pair through a molecular sieving mechanism. Column breakthrough measurements further demonstrate the efficient separation of linear nHEX from the mono- and dibranched isomers.