Abstract: In order to study the characteristics of zooplankton community in the important reaches and lakes of Three-River head-waters region in Qinghai Province, zooplankton and the main water quality indexes were investigated three times at the beginning of May, August and the end of September in 2017. The species structure and density composition of zooplankton in the study area were analyzed, and the water quality was evaluated by dominant species indication method. The results showed that there were 98 species of zooplankton, including 23 protozoans (23.4%), 51 rotifers (52.0%), 14 Cladocera (14.3%) and 10 copepods (10.2%). The species density of zooplankton was 0~3201ind./L, which from high to low were in September, August, May. The water quality of each monitoring section was good and the water was clean. In this study, the species density of zooplankton and evaluation of water quality were preliminarily evaluated, which is of great significance to the study of aquatic organisms of this region.