In this study, the effect of the position of anode on the efficiency and electricity generation of the novel anaerobic baffle reactor-bioelectricity Fenton (ABR-BEF) system were investigated for treatment traditional Chinese medicine (TCM) wastewater. The components of loosely-bound extracellular polymeric substances (LB-EPS) and tightly-bound extracellular polymeric substances (TB-EPS) in the sludge were also measured. Finally, the high-throughput sequencing technology was used to analyze the variation of microbial community in the system at different anode positions. The results showed that when the position of anode electrode was changed from the 4th compartment to the 3rd and 2nd compartment, the COD removal rate was reduced from 90% to 70% and 65%, respectively, due to the distance between anode and cathode gradually increasing. Meanwhile, the voltage output was declined from 149.8mV to 95.3mV and 50.0mV, and the maximum power density was decreased to 76.78mW/m³ to 55.57mW/m³ and 52.87mW/m³, respectively. However, the removal rate of catechol in the cathode chamber was remained around 95%. After changing the position of anode, the protein content in the LB-EPS and TB-EPS was decreased, especially TB-EPS. In addition, the polysaccharides content of LB-EPS and TB-EPS was the highest when the position of anode was changed into the 3rd compartment. When the position of anode was changed from the 4th compartment to the 3rd and 2nd compartment, the abundance of Methanothrix was increased to 71.09%, 72.47%, 58.03% and 76.79% in each compartment at the genus level of archaea. While the abundance of Deltaproteobacteria, which was a class contained electrogenic bacteria, was reduced to 2.54%, 6.06%, 4.40% and 4.87%, respectively. The increasing of the distance between anode and cathode was leaded to reduce the abundance of electrogenic bacteria, which was an important reason for the decrease of the electricity generation capacity of the ABR-BEF system.