In recent years, organic photocatalyst under visible-light absorption has shown significant potential for solving environmental problems. However, it is still a great challenge for constructing a highly active organic photocatalyst due to the low separation efficiency of photogenerated carriers. Herein, an effective and robust photocatalyst perylene-3,4,9,10-tetracarboxylic diamide/boron nitride quantum dots (PDI/BNQDs), consisting of self-assemble PDI with π–π stacking structure and BNQDs, has been constructed and researched under visible light irradiation. The PDI/BNQDs composite gradually increases organic pollutant photodegradation with the loading amount of BNQDs. With 10 mL of BNQDs solution added (PDI/BNQDs-10), the organic pollutant photodegradation performance reaches a maximum, about 6.16 times higher with methylene blue and 1.68 times higher with ciprofloxacin than that of pure PDI supramolecular. The enhancement is attributed to improved separation of photogenerated carriers from self-assembled PDI by BNQDs due to their preeminent ability to extract holes. This work is significant for the supplement of PDI supramolecular composite materials. We believe that this photocatalytic design is capable of expanding organic semiconductors’ potential for their applications in photocatalysis.