The diversity of plankton community in Danjiangkou Reservoir was investigated, water samples were collected from 9 locations in Danku, Hanku and tributary of Danjiangkou Reservoir in July 2020, based on single molecule real-time sequencing. The 18S and 16S gene were used to explore the diversity and community characteristics of eukaryotic and prokaryotic, respectively. Our study has found several aspects:(1) The dominant species of eukaryotic plankton community belong to Arthropoda, Streptophyta, Chlorophyta and Bacillariophyta. We identified the most widely distributed species with high relative abundance, include Cryptomonas curvata, Cryptomonas pyrenoidifera, Eudorina elegans etc., they all associated with the chemical oxygen demand. Thus, the chemical oxygen demand is the key environmental factor for the eukaryotic plankton community. (2) The dominant species of prokaryotic plankton community belong to Proteobacteria. Acinetobacter with high relative abundance is the indicator of sewage pollution, the important species Limnohabitans is associated with eutrophication. Cyanobacteria showed a low relative abundance, but bacteria associated with cyanobacteria like CL500-29_marine_group and hgcI_clade played a pivotal role in the prokaryotic community. Thus, the bioindicator showed the Danjiangkou Reservoir has risk in ecological health and needs further monitor. (3) The plankton community showed a high heterogeneity in different area, the tb-RDA analysis revealed the plankton community in Danjiangkou Reservoir can be divided into three different types, Danku type, Hanku type and tributary type, the difference was higher between different groups than within group, the roots of the difference between these groups lie in the different richness in the community. To sum up, the plankton community showed obvious spatial heterogeneity in Danjiangkou Reservoir, their community structure is associated with water eutrophication, organic pollution, sewage pollution etc., aquatic ecosystem monitoring should be strengthened urgently.