The rapid growth of nitrite-oxidizing bacteria (NOB) in reactor prevents the application of anaerobic ammonium oxidation (anammox) technology to main-stream wastewater treatment. How to eliminate NOB and reserve anaerobic ammonium oxidation bacteria (AnAOB) simultaneously becomes the biggest challenge. In this study two coupled biological aeration filters (BAFs) were built up to treat domestic sewage. In BAF1 nitrogen removal concentration was 21.4 mg/L via heterotrophic denitrification pathway. Backwash was conducted to BAF2 to improve nitrogen removal performance. After backwash Nitrospira proportion declined from 10.8% to 2.1%, while Candidatus Kuenenia percentage increased from 5.6% to 10.2%. Nitrogen removal concentration improved from 8.6 mg/L to 22.8 mg/L via anammox pathway in BAF2, and total nitrogen removal concentration reached to 44.2 mg/L in two coupled BAFs during aeration process. These findings could provide a new strategy for the application of anammox technology to main-stream wastewater treatment.