Trans-/cis-olefin isomers play a vital role in the petrochemical industry. The paucity of energy-efficient technologies for their splitting is mainly due to the similarities of their physicochemical properties. Herein, two new tailor-made anion-pillared ultramicroporous metal–organic frameworks (MOFs), ZU-36-Ni and ZU-36-Fe (GeFSIX-3-Ni and GeFSIX-3-Fe) are reported for the first time for the efficient trans-/cis-2-butene (trans-/cis-C4H8) mixture splitting by enhanced molecular exclusion. Notably, ZU-36-Ni unexpectedly exhibited smart guest-adaptive pore channels for trapping trans-C4H8 with a remarkable adsorption capacity (2.45 mmol∙g−1) while effectively rejecting cis-C4H8 with a high purity of 99.99%. The dispersion-corrected density functional theory (DFT-D) calculation suggested that the guest-adaptive behavior of ZU-36-Ni in response to trans-C4H8 is derived from the organic linker rotation and the optimal pore dimensions, which not only improve the favorable adsorption/diffusion of trans-C4H8 with optimal host–guest interactions, but also enhance the size-exclusion of cis-C4H8. This work opens a new avenue for pore engineering in advanced smart or adaptive porous materials for specific applications involving guest molecular recognition.