Polyoxometalates (POMs), that are well‐defined metal‐oxygen cluster anions, are functional molecules extensively used in various research applications. The synthesis of neutral purpurinimides, followed by conversion to cationic purpurinimides (CPIs), formed CPI–POM supramolecular complexes via electrostatic interactions between each CPI and the polyanionic POM. The cellular uptake of purpurinimides, CPIs, and their CPI–POMs in A549 and HeLa cell lines was confirmed by confocal laser scanning microscopy. CPIs showed concentration‐dependent dark cytotoxicity; however, CPI–POMs exhibited reduced low dark cytotoxicity. After photoirradiation, CPIs and CPI–POMs revealed enhanced photodynamic therapy (PDT) compared to free purpurinimides against A549 and HeLa cells. The CPIs exhibit low cell viability by incorporating their PDT effect with intrinsic dark cytotoxicity; however, the CPI–POMs exhibited a POM delivery effect‐based enhanced PDT activity in the supramolecular complex system with low dark cytotoxicity. In particular, the clicked CPI–POM revealed two times higher PDT activity compared with the clicked free CPI, due to the good delivery effect of POM.