Selective recognition of 1,3-butadiene from complex olefin isomers is vital for 1,3-butadiene purification, but the lack of porous materials with suitable pore structures results in poor selectivity and low capacity in C4 olefin separation. Herein, two sulfonate-functionalized organic frameworks, ZU-601 and ZU-602, are designed and show impressive separation performance toward C4 olefins. Benefiting from the suitable aperture size caused by the flexibility of coordinated organic ligand, ZU-601, ZU-602 that are pillared with different sulfonate anions could discriminate C4 olefin isomers with high uptake ratio: 1,3-butadiene/1-butene (207), 1,3-butadiene/trans-2-butene (10.1). Meanwhile, their layer-stacked structure enables the utilization of both intra- and interlayer space, enhancing the accommodation of guest molecules. ZU-601 exhibits record high 1,3-butadiene adsorption capacity of 2.90 mmol g-1 (0.5 bar, 298 K) among the reported flexible porous materials with high 1,3-butadiene/1-butene selectivity. The breakthrough experiments confirm their superior separation ability even for all five C4 olefin isomers, and the molecular-level structural change is well elucidated via powder, crystal analysis, and simulation studies. The work provides ideas toward advanced materials design with simultaneous high separation capacity and high separation selectivity for challenging separations.