In order to explore the wider applicability of microbial fuel cells, aerobic granular sludge (AGS) was coupled with microbial fuel cells (MFC) in this experiment, and the sequencing batch operation was adopted, the influent COD was fixed at 780 mg/L, and the C/N ratio was adjusted to 5, 10, 15, 20 by changing the concentration of NH4+ (39, 50, 78 and 156 mg/L), respectively. The influence of different C/N on microbial diversity and community structure in the cathode chamber of the system was studied. High-throughput sequencing analysis showed that the relative abundance of different bacterial communities in the cathode chamber changed significantly with the change of influent C/N. At the phylum level, the relative abundance of Proteobacteria was 45% when C/N=10. When C/N=20, it decreases to 41.1%. At class level, Deinococci with the largest variation in relative abundance can account for 27.2% at C/N=5, and only 15.1% at C/N=20. Under the conditions of C/N=15 and 20, the metabolic relative abundance of microorganisms in the cathode chamber was the highest (77.1%), and the corresponding metabolic strength of the cathode aerobic granular sludge was strong, which played an important role in the microbial degradation of COD.