Freshwater lakes encounter a series of problems, such as a decline in lake water quality, a sharp decrease in biodiversity, and ecological degradation. As such, lacustrine studies by highly skilled professionals and managers with water resources at home and abroad have focused on assessing the aquatic ecosystem health status of lakes. In this study, the health status of the aquatic ecosystem in the largest freshwater lake in China (Poyang Lake) was assessed, and its temporal and spatial characteristics were illustrated. The index contained three element layers, including hydrologic characteristics, trophic status, and aquatic organisms. The health status of the aquatic ecosystem was classified into three categories: ‘good’, ‘moderate’ (subhealthy), and ‘bad’. It was examined through extension evaluation method. Results showed ‘moderate’ health status, whereas remarkable seasonal and spatially variations. The annual changes in the health status were remarkably due to the influence of complex hydrological and hydrodynamic conditions. This study provides an overall understanding of the aquatic ecosystem evaluation in Poyang Lake. Such an understanding is vital for environmental conservation and identification of causes of the aquatic ecosystem degradation in Poyang Lake.