Photocatalytic fuel cell (PFC) is a newly developed cell device that can effectively convert chemical energy resulted from photocatalytic process into electrical energy. In this research, a novel composite functional dual-chambered photocatalytic fuel cell is designed and optimized. In the cathode chamber, the Fenton-like reaction is introduced to produce strong oxidizing OH center dot radicals, which thereby enhances the advanced oxidation of wastewater and is much faster than the anode reaction. Meanwhile, photo-induced charge transfer as well as electronic generation ability can be further improved compared with the system only with O-2 pumped in. With the help of this special PFC device, the electrode reactions can occur in two chambers independently, thus different types of organic substances can be degraded, accompanying with the generation of electrical energy simultaneously. According to the degradation of various dyes, it is found that the anode reaction is more suitable for the degradation of cationic dye rather than anionic dye, and just reverses for the cathode reaction. Among four selective types of dyes, the PFC shows the best purification effect to X3B, while the highest enhancement of electric output is found when methylene blue (MB) is employed.