In this study, a novel anaerobic baffled reactor-bioelectricity-Fenton (ABR-BEF) coupling reactor, combining an ABR, microbial fuel cell (MFC), and Fenton system, was used to treat traditional Chinese medicine (TCM) wastewater containing catechol. The bio-electrochemical degradation of the catechol reached 99.7% after 8 h at dissolved oxygen (DO) concentration of 4 mg/L in the cathodic chamber. The removal rates of chemical oxygen demand (COD) reached 91.7%, when the ratio rate was 1 and the DO concentration was 4 mg/L. Moreover, the maximum open-circuit voltage and power density of the coupling reactor reached 424.9 mV and 77.1 mW/m3, respectively. According to the PICRUSt analysis, carbohydrate metabolism took up the most abundant function of metabolism and the enrichment of membrane transporters may relieve TCM wastewater toxicity. These results suggest that the ABR-BEF coupling reactor could be applied as an efficient approach to treat TCM wastewater.