Due to the increasing problems of lake ecology, the security state of lake ecosystem has become a hot issue of people's attention. It is particularly important to understand the status of lake ecosystem and carry out precise management, ecological restoration and protection according to its health status. Based on the long-term monitoring data and other data collected on the ecological environment of Lake Poyang and its watershed, this paper constructed an indicator system for lake health assessment from six aspects:physical form, hydrology, aquatic environment, water area ecology, wetland ecology and social services by using comprehensive indicator system method. It covered 26 indexes, such as lake entrance condition, variation degree of runoff from five inflow rivers to the lake, and water quality compliance rate (as to national creteria) of rivers to the lake. According to the set threshold level, the health status of each level of Lake Poyang ecosystem health was evaluated, and the scores of the criteria layer and the target layer were obtained by weighting scores of each index of lake ecosystem. Finally, the objective evaluation of Lake Poyang ecosystem health was carried out. The results showed that the constructed system had strong pertinence, comprehensive science and operability, and could provide a case and method reference for the ecosystem health evaluation of Lake Poyang and similar Yangtze river-connected lakes. The evaluation results showed that the target level score of Lake Poyang health signs was 73.45, and the evaluation result was sub-healthy. The health of Lake Poyang aquatic ecosystem was mainly affected by discharge capacity, hydrological regime change, eutrophication degree and species diversity. Finally, according to the aquatic ecosystem health rating of Lake Poyang, this paper raised some problems that need to be solved in Lake Poyang aquatic ecosystem protection, and puts forward countermeasures and suggestions for its protection.