Based on the element analysis of lacustrine sediments and surface soils in Chaiwopu Lake watershed, Xinjiang, the geochemical characteristics and potential ecological effects of the heavy metals are discussed with the methods of mathematical statistics. Associated with the principal component analysis (PCA) and correlation analysis of element contents from Chaiwopu Lake sediment core, the change of element content including Al, K, Na, Be, Ba, Ti, Ca, Mg and Sr was controlled by the regional chemical weathering intensity. The correlations are significant positive between the heavy metals (Fe, Mn, Zn, Cu, Cr, Ni, Pb and Cr), the organic matter content and the content of clay fraction. Before 1950 with the background of weak human activity, the heavy metals are controlled by the watershed hydrodynamics. In the period of last 50 years with strong human activities, the anthropogenic sources resulted in high loadings of heavy metals. With the constrained incremental sum of squares cluster analysis (CONISS) and cluster analysis of element contents of surface soils and lacustrine sediments, the geochemical composition characteristics were analyzed, which showed that the element contents recorded the impacts of human activity and natural environmental change. Finally, the potential ecological risk assessment of heavy metals (Cu, Cr, Zn and Pb) was evaluated. The results showed Cu and Pb were the more harmful heavy metal species in the studied areas, but the potential ecological risk of the whole heavy metals was slight.