Inthis research, a new system that combination of the ion exchangemembrane and ultrafiltration membrane (IEM-UF) nitrogen enrichment with shortcut nitrification and denitrification was proposed for low carbon nitrogen ratio of domestic sewage. The performance of nitrogen and COD removalin the system were studiedunder the three stage operating condition. Meanwhile, the characteristicsof the microbial community in the system were analyzed by high throughput technology, andthe effect of the flora changes on the nitrogen removal was investigated. The rate of nitrite accumulation in the shortcut nitrification reactor reached above 90%only 19d when C/N was 3and DO=0.5mg/L.When the ratio of denitrifying influent was 2:1, the average removal rates of COD and NO_x^--Nreached above 80% and 89%, respectively. The maximum removal rate of TN was above 64.8%. Besides, the change of bacterial community structure in the three stage was consistent with the change of nitrogen removal efficiency. Under the three operatingconditions, the proportion of Nitrosomonas accounted for the proportion of the genus in the shortcut nitrification reactor was about 3.69%, 5.48% and 0.53% respectively. As well asthe sum of denitrifying bacteria Dechloromonas and Thauera in the denitrification reactor accounted for 33.35%, 25.62% and 20.52%, respectivelyunder the three stage.