A dramatic enhancement of organics degradation and electricity generation has been achieved in a wastewater fuel cell (WFC) system via strengthening superoxide radical with radical chain reaction by using a novel 3D anthraquinone/polypyrrole modified graphite felt (AQS/PPy-GF) cathode. The AQS/PPy-GF was synthesized by one-pot electrochemical polymerization method and used to in-situ generate superoxide radical by reducing oxygen under self-imposed electric field. Results showed that methyl orange (MO) were effectively degraded in AQS/PPy-GF/Fe2+ system with a high apparent rate constant (0.0677 min−1), which was 3.9 times that (0.0174 min−1) in the Pt/Fe2+ system and even 9.4 times that (0.0072 min−1) in the traditional WFC system (without Fe2+). Meanwhile, it showed a superior performance for electricity generation and the maximum power density output (1.130 mW cm−2) was nearly 3.3 times and 5.0 times higher, respectively, when compared with the Pt/Fe2+ system and traditional WFC. This dramatic advance was attributed to 3D AQS/PPy-GF cathode which produces more O2− via one-electron reduction process. The presence of O2− cannot only directly contribute to MO degradation, but also promotes the final complete mineralization by turning itself to OH. Additionally, O2− accelerates the Fe2+/Fe3+ couple cycling, thus avoiding continuous addition of any external ferrous ions. Inhibition and probe studies were conducted to ascertain the role of several radicals (OH and O2−) on the MO degradation. Superoxide radicals were considered as the primary reactive oxidants, and the degradation mechanism of MO was proposed. The proposed WFC system provides a more economical and efficient way for energy recovery and wastewater treatment.