Effective separation of hexane (C6) isomers is critical for a variety of industrial applications but conventional distillation methods are energy-intensive. Adsorptive separations based on porous coordination polymers (PCPs) offer a promising alternative due to their exceptional porosity and tunable properties. However, there is still an urgent need to develop PCPs with high stability and separation performance. This study investigates how substituting a methyl (-CH3) group with a trifluoromethyl (-CF3) group can regulate pores and hydrophobicity in PCPs. This precise adjustment aims to enhance stability and improve the kinetic separation performance of hydrophobic C6 isomers by considering the size and hydrophobicity of the trifluoromethyl group. Two isostructural PCPs with pcu topology, PCP-CH3 and PCP-CF3, were synthesized to vary pore diameters and hydrophobicity based on the presence of -CH3 or -CF3 groups. PCP-CF3 showed greater stability in water compared to PCP-CH3. While PCP-CH3 had high adsorption capacities, it lacked selectivity, whereas PCP-CF3 demonstrated improved selectivity, particularly in excluding dibranched isomers. Dynamic column separation experiments revealed that PCP-CF3 could selectively adsorb linear and monobranched isomers over dibranched isomers at room temperature. These findings highlight the potential of fluorine-modified PCPs for efficient isomer separation and underscore the importance of stability improvement strategies.