In order to understand the spatial distribution and ecological risk of heavy metal pollution in the sediments of the Three Gorges Reservoir, surface sediment samples in six typical tributaries and estuaries were analyzed. The heavy metal content in sediment was detected by ICP-MS (PE Elan DRC Ⅱ, PerkinElmer, Waltham, MA, USA) after digestion by mixed acid. The data were evaluated and analyzed using multiple methods, including the potential ecological risk index, the geoaccumulation index (Igeo), and cluster analysis. The results show that the tributary surface sediments were polluted by heavy metals to a certain extent. Cu, Zn, Pb, and Cr have been enriched in sediments in recent years. The results of Igeo show that the pollution degree is as follows: Pb > Cu > Zn > Cr > Cd > Ni > As > Hg. According to the potential ecological risk index, the grades of Yunyang, Xiaojiang, and Xinjin are all medium risk, and Cd has the highest contribution rate. Combined with field investigation data, cluster analysis, and correlation analysis, we conclude that Cu, Zn, and Cr are likely to come from agricultural chemical fertilizers and industrial sewage, while Pb mainly comes from the discharge of ship fuel.