Sediment microbial communities play crucial roles in biogeochemical cycles of aquatic systems, and knowledge of microbial community structure could improve our understanding of these roles. To the best of our knowledge, there is no study revealing the compositions and functions of bacterial communities in sediments of the Danjiangkou Reservoir so far. In this study, 5 surface sediment samples were collected from the reservoir in May 2017. High-throughput sequencing was performed to analyze the distribution characteristics of the community structure and diversity of bacteria, and their relationship with environmental factors. Phylogenetic analysis based on 16S rDNA sequences showed that bacterial communities could be divided into 33 major phylogenetic groups. The dominant phylogenetic groups included Proteobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, Nitrospirae, Acidobacteria, Planctomycetes and Omnitrophica. The results of redundancy analysis (RDA) for the relationship between the 33 bacterial phyla and 7 environmental factors showed that the pH, total phosphorus, sediments organic matter, and ammonium nitrogen were the main environmental factors affecting the distribution characteristics of the bacterial community. Spearman correlation analysis was employed to explore associations between all bacterial genera and environmental factors; the genera significantly correlated with the environmental factors mainly belonged to the phylum Proteobacteria. PICRUSt was used to understand the metabolic and functional abilities of the observed bacterial communities. The results obtained showed wide genetic diversity of organisms involved in various essential processes, such as energy production and conversion, signal transduction mechanisms, amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, translation, ribosomal structure and biogenesis, replication, recombination and repair. The surface sediments of the Danjiangkou Reservoir can be ranked in the following order based on the 16S rRNA gene copy number of the detected phylotype:Taizishan > Songgang > Kuxin> Qushou > Heijizui.