In this study, the enclosure system exhibited perfect nitrogen removal performance with in situ oxygen-enhanced indigenous aerobic denitrifying bacteria in an enclosure experiment. We explored changes in the microbial community during the nitrogen removal process using the MiSeq high-throughput sequencing technology. The results revealed a total of 7974 and 33653 operational taxonomic units (OTUs) for water and sediment systems, respectively, with 97％ similarity. The OTUs were found to be affiliated with eight main phyla (Proteobacteria, Acti-nobacteria, Cyanobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Firmicutes, and Actinobacteria). The diversity of the enhanced system was found to be higher than that of the control system. Principal component analysis (PCA) revealed that significant spatial and temporal differences were exhibited in the microbial community during nitrogen removal in the enclosure experiment. Redundancy analysis (RDA) indicated that physical parameters (temperature, dissolved oxygen, and pH), nitrogen (total nitrogen and nitrate), functional genes (nirK and nirS ), and dissolved organic carbon (DOC) were the most important factors affecting bacterial community function and composition. Lastly, the results suggested that the variation in the microbial community could be analyzed through the MiSeq high-throughput sequencing technology, which may provide technical support for future field tests.