Abstract: Different kinds of active biochar were prepared from cyanobacteria in Taihu Lake and put into the cathode of bioelectrochemical system (BES) to promote hydrogen autotrophic denitrification. Three groups of cyanobacterial biochar of Unmodified (ABC-800), modified by nitric acid (ABC-800N) and modified by KOH (ABC-800K) were observed by scanning electron microscopy (SEM), energy dispersive spectrometer (EDS) and Fourier transform infrared spectroscopy (FTIR), and were compared with the control group without the addition of cyanobacteria biochar, to investigate the electron transfer mechanism in denitrification process of biochar promotes BES biocathode. The results showed that the contents of nitrogen and oxygen on ABC-800N surface were the highest, and the abundance of conjugated quinone and ketone structures related to electron transport capacity and biocompatibility was also the highest. Adding cyanobacteria biochar to the abiotic cathode of BES could improve the nitrogen removal efficiency of the cathode. After adding 0.5 g ABC-800N into the BES abiotic cathode, the nitrogen removal efficiency reached the highest within 7 days, which was 96.0%, while the control group was only 29.6%. High-throughput sequencing showed that the dominant bacteria in ABC-800N group were Thauera, JGI_0001001_H03, Thiobacillus, and Denitratisoma, etc.