Abstract: The population and economy in Yangtze Economic Belt accounts for more than 40% of whole China. Balancing the relationship between development and management of the water systems of Dongting Lake in the Yangtze River Basin is an important link in implementing the principle of promoting well-coordinated environmental conservation and avoiding excessive development. In order to understand the characteristics and ecological risks of heavy metal pollution in Dongting Lake water system, 24 sediment samples were collected in August, 2017. The content characteristics and the pollution status of heavy metals in the study area were analyzed by the method of Igeo, RI and mPEC-Q, and the interrelation and source of heavy metals were evaluated by CA and PCA. The results showed that:① The concentrations of heavy metals in the surface sediments from high to low were Cr, Pb, Cu, As, Cd, Hg. The concentration of Hg, Cr, Cd, Pb, Cu were 7.0, 2.0, 9.3, 2.2, 2.3 times of the background values, respectively. The average concentration of Hg, As, Cr, Cd, Pb in surface sediments of the lake areas were 1.1～1.5 times of that in the main inflowing rivers.② The results of geo-accumulation index method and the potential ecological risk evaluation indicated that Cd and Hg were considered as the dominant pollutants. The RI values from high to low were Cd, Hg, Cu, Pb, As, Cr. The mean value of mPEC-Q was 0.43, indicating that the sediments in all of the sampling sites had a 15%-29% probability of toxcity.③ Source analysis showed that As, Pb, Cd and Cu were homologous and mainly came from the industrial wastewater from the Xiangjiang River, Zijiang River, Yuanjiang River, and Lishui River, indicating that further promoting the transformation and upgrade of enterprise is necessary, and the practical application of biological snail control should be strengthened to reduce the concentration of Cr.