In order to explore the microbial mechanism of treatment effect changes affected by iron-rich media in the biological aerated filter (BAF) at low temperatures, contrast experiment was used to investigate the number of nitrifying bacteria and bacterial community diversity in control group without iron-rich media and experimental group with iron-rich media. The results showed that when the temperature decreased from 14 ℃ to 12 ℃, the removal rate of COD, NH+4—N, TN and TP in the control group decreased by 4.17%, 4.67%, 4.87% and 10.86%, respectively. At 14 ℃, the removal rate of COD, NH+4—N, TN and TP in the experimental group were 2.35%, 2.37%, 10.86% and 52.34% higher than those in the control group. When the temperature decreased from 14 ℃ to 12 ℃, the removal rate of TN and TP in the experimental group decreased from 45.98% and 97.74% to 42.33% and 91.55%, respectively, which were 12.08% and 57.01% higher than those in the control group at 12 ℃, and still 7.21% and 46.15% higher than those in the control group at 14 ℃. At 14 ℃, the abundance of Nitrosomonadales, Xanthomonadales and Rhodocyclales in the middle bioflim of the experimental group were 3.1%, 2.3% and 2.9% higher than those of the control group, respectively. The decrease of the temperature can reduce the number of nitrifying bacteria in BAF, which can be remedied by the use of iron-rich media, because it is beneficial to increasing the number of nitrifying bacteria in BAF, as well as the abundance of Nitrosomonadales, Xanthomonadales and Rhodocyclales. The increase of these bacteria can weaken the adverse influence of low temperature on BAF treatment effect.