Abstract: At present, most of the studies on heavy metals in the sediments of Dianchi Lake focus on the surface sediments, but there are few studies on the vertical distribution of heavy metals. Concentrations of four kinds of heavy metals including Zn, Cu, Cr and Cd in the sediments of 12 different areas of Dianchi Lake were investigated with flame atomic absorption spectrometer. Vertical distribution of the metals in the lake sediment were analyzed. The differences degree of heavy metal pollution in Caohai sub-lake and Waihai sub-lake were discussed. Pollution of heavy metals in sediment was analyzed by geological accumulation index method and Hakanson Potential Ecological Hazard Index method. Results show that: the concentrations of heavy metals in sediment of Caohai sub-lake are higher than those in sediment of Waihai sub-lake. The order of average mass ratio of four heavy metals in sediment of Waihai sub-lake are Zn > Cu > Cr > Cd, while the order of average mass ratios of four heavy metals in Caohai sub-lake are Zn > Cu > Cr ≈ Cd. Except Cr, the concentrations of other three metals decrease with increasing depth in the sediments of Caohai sub-lake. This trend is not obvious in Waihai sub-lake. Assessment results based on geo-accumulation index and potential ecological risk index show that the pollution status of Cd is the most serious, followed by Zn and Cu, and the pollution degree of Cr is minimum in all sampling sites. The pollution status of Caohai sub-lake is more serious than that of Waihai sub-lake. From the south area to the north area, the metal pollution becomes more and more serious in Caohai, while the pollution is decreased near the Wujiadui wetland park. There is no obvious change of the heavy metal pollution with the change of region in the Waihai sub-lake.