In this study, the biocathode microbial fuel cell was constructed by using anion exchange as separator, which could remove ammonia nitrogen by simultaneous nitrification and denitrification process, degrade acetone and generate electricity. We investigated the effects of different acetone concentrations such as 50 mg/L, 100 mg/L, 300 mg/L, 500 mg/Land 700 mg/L on electricity generation and removal rate of ammonia nitrogen (200mg/L) for MFC. The results showed that the removal rate of acetone was more than 96% with the selected concentration. When the concentration of acetone was higher than 300 mg/L, the removal of ammonia nitrogen would be inhibited, and the highest removal rate of ammonia nitrogen was 73.7%. Besides, when acetone concentration was 300 mg/L, the corresponding MFC can achieve the highest power density of 49.7 mW/m2. High throughput sequencing technology was used to analyze the microbial community structure of anode and cathode. At the phylum level, the dominant microbial communities of anode were mainly Proteobacteria, Bacteroidetes and Firmicutes. While the dominant microbial communities of cathode were Bacteroidetes, Actinobacteria, Proteobacteria and Acidobacteria. At the genus level, the dominant bacteria of anode were Comamonas, Acetoanaerobium，Stenotrophomonas, while the dominant bacteria of cathode were Rhodoccus, Aridibacter, Thauera，Ignavibacterium.