In this study, the combination of strengthen circulation anaerobic (SCA) and biological aerated filter (BAF) reactor was employed to treat municipal wastewater. Different reflux percentages or gas/water ratios were selected for evaluating the removal performance of contaminants in SCA-BAF system and sequential nitrification and denitrification process in BAF reactor. In general, reflux percentage (200%) and gas/water ratio (3:1) were a relatively suitable operational condition for BAF reactor. The COD, NH3-N, TN concentrations of effluents collected from BAF reactor varied in the ranges of 18-80, 0.2-7.2, 9.1-33.0 mg L-1, respectively. A higher NO3-N concentration in effluents of BAF reactor resulted from the lack of organic carbon resource in wastewater. High throughput sequencing analysis indicated that different nitrification and denitrification bacteria thrived in the BAF reactor. The DO, NO2-N and NO3-N concentrations showed a strong correlation with Nitrospira and Nitrosomonas in bacterial samples outlet (c and e) under gas/water ratio of 3:1.