The Danjiangkou reservoir is the main source of water for the "middle-route" of the South to North Water Diversion Project in China. Its water quality directly affects the safety of drinking water for residents along this route. In this study, 15surface-water samples were collected from the reservoir at low-water period (January) in 2016, and 12 essential environmental factors were investigated. The results showed that the water quality in the reservoir was strongly influenced by total nitrogen (TN) and the permanganate index, with the water quality being ranked at IV or Ⅱ for all locations. The water in this reservoir was in the mesotrophic state. The high-throughput sequencing approach was adopted to analyze the distribution characteristics of the community structure and diversity of bacterioplankton and their relationship to environmental factors. Phylogenetic analysis based on 16S rDNA sequences showed that bacterioplankton could be divided into 22 major phylogenetic groups. The dominant phylogenetic groups included Actinobacteria, Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, and Acidobacteria. At the genus level, the dominant phylogenetic groups included CL500-29 marine group, hgcI clade, Fluviicola, Sediminibacterium, Flavobacterium, LD28 freshwater group, Limnohabitans, Synechococcus, Bacillus, and Cyanobacteria norank. Diversity of the bacterioplankton community in the Danjiangkou reservoir can be ranked in the following order:Heijizui > Taizishan > Kuxin> Songgang > Qushou. The results of canonical correspondence analysis (CCA) for the relationship between the 22 phyla of bacterioplankton and 12environmental factors showed that the T, pH, NH₄⁺-N, and SD were the main environmental factors affecting the distribution characteristics of the bacterioplankton community.