A novel IBAF system (altered conventional biological aerated filter (BAF) for intermittent aeration) was used to treat BDD anodes electrochemical oxidation gasification wastewater effluent, after which 454 pyrosequencing was applied to investigate the bacterial community of IBAF and demonstrate the relationship between dissolved oxygen (DO) and the bacterial community. The results showed that the concentration of COD, NH4+-N and NO3--N reached 55.08, 7.64 and 7.76 mg/L, respectively, in IBAF effluent because of changes in the DO concentration at 30 days after system start-up. The bacterial community results revealed that the 40 cm sample had the highest bacterial diversity. The bacterial species were approximate in total samples at phylum and family level, but the relative abundance was significantly different because of change in DO concentration. In addition, sample distance analysis indicated that the similarity of different samples was related to the DO concentration at different heights.