In this study, a three-stage biological aerated filter (BAF) system was proposed for the enhancement of nitrogen removal in the treatment of low carbon-to-nitrogen ratio (C/N ratio) municipal wastewater. Operational parameters were studied for each process for maximum nitrite accumulation in the nitrification step and nitrite adaptation in the denitrification step. Nitrite accumulation during nitrification could be controlled by the dissolved oxygen (DO) concentration, presenting a mean value of 40% at around 1.0mg DO/L. Denitrification could be adapted to nitrite and the process was stable if nitrite in the reactor was keep low. Once the operational parameters were established, the process was stable and a steady state was maintained for over 30 days, and the various indexes of discharged water were up to the Discharge standard of pollutants for municipal wastewater treatment plant (GB18918-2002) Level-one A. It was concluded that the three-stage BAF system proposed in this study was excellent in nitrogen removal performance by employing three-column functioning as short-cut nitrification, short-cut denitrification and secondary nitrification, respectively.