Assessing the aquatic ecosystem health status of lakes has been the focus of lake studies for domestic and overseas researchers and water resource managers. Poyang Lake, which is one of the only two remaining large Yangtze-connected lakes in the middle reaches of Yangtze River in China, provides considerable ecosystem service functions, such as flood water storage, water supply for industrial and agricultural production, maintenance of the unique and diverse biota of the entire Yangtze floodplain ecosystem, maintenance of regional ecological balance and so on. However, due to the impact of climate change and human activities, Poyang Lake has experienced drastic hydrological changes, water quality decline and aquatic ecological function degradation in recent years. An assessment of the aquatic ecosystem health of Poyang Lake is of great importance. On the basis of the index system construction principles and a meta-analysis of previous research, this paper puts forward the index system for the ecosystem health assessment of Poyang Lake. The indices contains the three element layers of aquatic organisms, hydrologic characteristics and trophic status and the five indicators of ratio of cyanobacteria biomass to diatom biomass (CB/DB), diversity index of macrozoobenthos, lowest water level anomaly during the dry season, mean water level anomaly during rising season and trophic state index (TLI). Then, the thresholds of indicators are determined using empirical study, frequency analysis, standard specification and so on. Aquatic ecosystem health status is categorised into three groups: 'good', 'moderate' and 'poor'. The study could provide theoretical basis for identifying the causes of the lake aquatic ecosystem health degeneration and protecting the environment of Poyang Lake. This present study provides an attempt to quantify the aquatic ecosystem health in a large floodplain lake with dramatic hydrological variations and will give some impetus for floodplain ecosystem assessment and management worldwide.