Xylene isomers are crucial chemical intermediates in great demand worldwide; the almost identical physicochemical properties render their current separation approach energy consuming. In this study, we utilized the soft porous coordination polymer (PCP)'s isomer-specific structural transformation, realizing o-xylene (oX) recognition/separation from the binary and ternary isomer mixtures. This PCP has a flexible structure that contains flexible aromatic pendant groups, which both work as recognition sites and induce structural flexibility of the global framework. The PCP exhibits guest-triggered "breathing"-type structural changes, which are accompanied by the rearrangement of the intraframework π-π interaction. By rebuilding π-π stacking with isomer species, the PCP discriminated oX from the other isomers by its specific guest-loading configuration and separated oX from the isomer mixture via selective adsorption. The xylene-selective property of the PCP is dependent on the solvent; in diluted hexane solution, the PCP favors p-xylene (pX) uptake. The separation results combined with crystallographic analyses revealed the effect of the isomer selectivity of the PCP on xylene isomer separation via structural transition and demonstrated its potential as a versatile selective adsorptive medium for challenging separations.