Abstract: Hongze Lake, which located in the lower reaches of the Huaihe River, is the fourth largest freshwater lake in China and an important node of the eastern route of South to North Water Diversion Project. In recent years, the heavy metal pollution of Hongze Lake has attracted much attention. The author analyzed the present situation and main sources of heavy metal pollution in Hongze Lake, and putted forward the control countermeasures. The results show that the overall pollution level of Hongze Lake is relatively light. However, the spatial distribution of the pollution is quite different. Cd pollution is serious and As pollution is increasingly significant, which need more attention. The main sources of heavy metals in Hongze Lake include water and sediment input from Huaihe River, the water regulation from south to north, non-point source pollution of farmland and aquatic products breeding. Prevention and control of heavy metal pollution in Hongze Lake should be focus on: reducing heavy metal input from Huaihe River; optimizing distribution and standardizing breeding of aquatic products; precisely fertilizing and applying pesticide to control agricultural non-point source pollution; implementing heavy metal migration and transformation control technology and pollution remediation technology.