This study focused on an iron phthalocyanine compound with aligned CNTs on the surface of a carbon felt electrode (FePc/CNT/C) to enhance the bio-electro-Fenton microbial fuel cell system cathodes reaction rate of hydrogen peroxide and the electrical plate. Experiments of polarization curves and power density, decolorization of Reactive Black 5 (RB5), and scanning electron microscopy (SEM) measured the characteristics of the cathode plate. FePc/CNT/C presented better electrical properties (open-circuit voltage, maximum current density, and maximum power density) than that of CNT/C and C, as FePc is a catalyst and its planar structure could easily adhere to CNT to enhance the reduction reaction at the cathode and provide higher specific surface area. The optimal decolorization of RB5 dye, as achieved with the FePc/CNT/C electrode, was 61.79% among the three cathode electrodes in the bio-electro-Fenton microbial fuel cell system, and the maximum number of hydroxyl radicals was generated for the cathode electrode of FePc/CNT/C. These results suggest that the bio-electro-Fenton microbial fuel cell system could be applied as an energy-saving and efficient approach for dye-containing wastewater treatment.