Incorporating local mobility into a flexible framework promises to create cooperative properties unattainable in a conventional soft porous crystal. In this study, we propose a design strategy that integrates substituent moieties and a flexible porous crystal framework via intra‐framework π–π interactions. This integration not only facilitates framework structural transitions but also gives the porous coordination polymers (PCPs) different guest‐free structures that depend on the activation conditions. The incorporated flexibility gives the material the ability to discriminate C6 alkane isomers based on different gate‐opening behaviors. Thus, the PCP has potential applications in C6 isomer separation, a critical step in the petroleum refining process to produce gasoline with high octane rating. This strategy, based on ligand designability, offers a new approach to flexible PCP structural and functional design.