The development of organic supramolecular photocatalytic materials requires a deeper understanding of the structure-activity relationship. Herein, the effects of H/J-type stacking on the photocatalytic mechanism and activity of PDI have been investigated. As a face-to-face arrangement, H-aggregates have higher pi-electron conjugation and show more semiconductor characteristics, which results in higher carrier separation and migration efficiency under irradiation. Whereas; J-aggregates exhibit more molecular properties due to its low pi-electron conjugation caused by head-to-tail stacking mode. As a result, H-aggregated PDI mainly forms superoxide radicals (center dot O-2(-)) and holes (h(+)) through electron-transfer (ET). In contrast, J-aggregated PDI mainly generates singlet oxygen species (O-1(2)) via energy-transfer (EnT). Benefit from the stronger oxidizability of center dot O-2(-) and h(+), H-aggregated PDI shows higher photocatalytic activity for small molecule degradation and oxygen evolution under visible light. Whereas, J-aggregated PDI exhibits potential application in photocatalytic anticancer treatment owing to its high O-1(2) quantum yields (0.66) under red light radiation. Our findings may provide a guidance for the development of supramolecular organic photocatalytic materials.