Abstract: In order to study the changes of microbial diversity and the correlation between microbial community structure and environmental properties in different periods of time, Fuling County, Zhongxian County and Wanzhou County, the middle section of the Three Gorges Reservoir area, were chosen as the research area. The water quality analysis and 16S rRNA high-throughput sequencing was used to study the microbial diversity of the sampling points during the high water period (January, March) and the low water period (May, July, September) in 2018, and the correlation between microbial community structure and environmental factors in different periods was analyzed. Results showed that the microbial diversity of Fuling in the upper reaches of the middle section of the Three Gorges Reservoir was higher than that of Zhongxian and Wanzhou in the middle and lower reaches. According to the analysis of community composition, the dominant bacteria in the middle section of the reservoir area did not differ significantly at the phylum level. The main dominant bacteria were Proteobacteria(80.50%～21.51%),Actinobacteria(32.60%～9.98%),Bacteroidetes(6.89%～3.50%),Cyanobacteria(9.65%～0.08%), etc. The composition of the microbial community has significant temporal variability, for example, the relative abundance of Actinobacteria, Firmicutes, Planctomycetes and Cyanobacteria was higher in the high water period than in the low water period, while the relative abundance of Proteobacteria was lower in the high water period than in the low water period. Redundancy analysis indicated that total nitrogen, dissolved oxygen and water level were the main environmental factors affecting microbial community structure in the middle section of the Three Gorges Reservoir.