The concentrations of heavy metals (Cu, Zn, Pb, Cd, Ni, Cr, As) in the surface sediment of Liangtan River were determined by using atomic absorption spectrometry (AAS) and atomic fluorescence spectrometry (AFS), and the toxic effects and sediment pollution assessment were conducted systematically by using Sediment Quality Guidelines (SQG), Hakanson Potential Ecological Risk Index. Moreover, the underlying source of heavy metal was analyzed. The results indicated that the concentrations of Cu, Zn, Pb, Cd, Ni, Cr, As were 29.4-158.1, 40.2-291.3, 23.4-148.2, 0.01-0.79, 6.4-106.2, 17.9-170.6, 1.3-45.1mg/kg respectively. Base on the SQG, besides Cd concentrations of few sampling sites were above the threshold effects level (TEL), the rest heavy metal concentrations of most sampling sites were all between TEL and the probable effects level (PEL), and biological toxicity effects may take place, especially Baishiyi, Hangu and Huilongba, harmful biological toxicity effects may frequently take place. Compared to background values of soil heavy metals in the Three Gorges Reservoir Region, the heavy metals in Liangtan River sediments showed higher ecological risk, and the ecological risk of the heavy metals, arranged from the highest to lowest pollution degree, was as follows Cd, As, Cu, Pb, Ni, Zn, Cr.