This paper is the result of environmental geological survey engineering. [Objective] Eastern Yunnan is an important coal base in southern China. To reveal the sources and ecological risks of heavy metals in sediments of small watersheds in typical coal mining areas is of great significance for the protection and treatment of ecological environment in coal mining areas. [Methods] The surface sediment samples were collected from small watersheds, and total contents of As, Cd, Cu, Pb, Hg, Mn, Ni, Cr, Zn and V were determined. The pollution degree and potential ecological risk of the heavy metals were evaluated by the geo- accumulation index and potential risk index, and their potential sources were analyzed based on mathematical statistics method. [Results] The results shows that the heavy metals in the sediments of small watershed exceed the soil background value of Yunnan Province except As and Pb, but only the average content of Cu exceed the risk screening value. In terms of spatial distribution, Cr, Ni and V are of medium variation while the other heavy metals are of highly variation. The pollution degree of each heavy metal can be ranked as Cr > Cu > Cd > Mn > Zn > V > Ni > Hg > Pb > As, in which the pollution of Cr is of moderate degree, the pollution of Cu, Cd, Mn, Zn, V and Ni are of mild degree, and the pollution of As, Pb and Hg are clean and pollution-free. The potential ecological risk of heavy metals in sediments presents a low risk to medium risk. Cd and Hg are the main ecological risk factors, showing moderate risk, while the ecological risk of other heavy metals is relatively low. The results of correlation analysis, principal component analysis and cluster analysis show that the contents of heavy metals in sediments are controlled by human activities and natural background, in which Mn, Ni, V and Cr are mainly from natural sources, As, Hg, Cd and Pb are mainly from man-made sources, and Cu and Zn are comprehensively affected by both of natural and manmade sources. [Conclusions] Although the study area is a typical geological high background area in eastern Yunnan, the potential risks caused by human activities such as coal industry to the ecological environment quality of sediments in the basin cannot be ignored, especially the monitoring and treatment of Cd and Hg.