Abstract:[Background] Biological aerated filter performs well on organic matter and ammonia nitrogen removal, whereas exhibits bad on phosphorus removal. [Objective] To improve the phosphorus removal efficiency of the BAF system. [Methods] The experimental group was an A/O filter, followed by a limestone-filling filter column. The control group was an identical one only without limestone filter. The treatment efficiency of reflux BAF system in experimental group and control group was compared and analyzed. Additionally, based on MPN method and high-throughput sequencing technology, the nitrifying bacteria quantity and microbial community structure in aerobic column were also investigated. [Results] Comparative tests showed that, compared with the BAF system without reflux, the removal efficiency of the reflux BAF system for COD, NH4+-N, TN, and TP increased by 3.16%, 41.21%, 40.62% and 18.93%, respectively. The removal efficiency of COD, NH4+-N, TN and TP in the experimental group increased by 1.75%, 2.3%, 2.2% and 23.1%, respectively. According to the results of high-throughput sequencing, the abundance of Proteobacteria, Actinobacteria, Firmicutes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Xanthomonadaceae in the aerobic filter column of the experimental group increased by 25.2%, 4.8%, 5.5%, 7.4%, 7.3%, 12.0% and 6.6%, respectively, compared with the control group. Meanwhile, the amount of different species between the experimental group and the control group at the genus level was 170. [Conclusion] The removal efficiency of TN and TP could be significantly improved by the reflux of limestone filter column. Calcium ions could improve the removal efficiency of phosphorus by chemical precipitation, and enhance the effect of biological phosphorus removal by improving the structure of bacteria in aerobic column.