Cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), zinc (Zn) and lead (Pb) of filtered water in 22 sampling sites and surface sediments of 18 sampling sites in Taihu Lake were measured with inductively coupled plasma mass spectrometry (ICP-MS). Meanwhile, in filtered water and surface sediments, the pollution evaluation were conducted by using singer factor pollution (Ii), intergrated Nemerow pollution index (I), index of geoaccumulation (Igeo), potential ecological risk index (RI) and mean potential effects concentration quotient (mPEC-Q), respectively. The results showed that the contents of Cu, Ni and Zn were the highest in filtered water except S3, S4, S20 and S22 sampling sites. The sequence of heavy metals content levels: Zn>Ni>Cu>Cr>Cd>Pb. The Ii and I values in the study area were less than 1, indicating that five heavy metals (Ni has no standard limit) were in clean condition in all sampling points. The contents of the six elements in the surface sediments exceeded the local background values, and the sequence of average contents: Zn>Cr>Pb>Ni>Cu>Cd, and at S12 sampling point (Fisherman’s Ecological Park), the content of the six elements were the highest. They had the largest Igeo, RI (327) and mPEC-Q (0.605), indicating that there were different degrees of pollution in sediments. The results of source analysis showed that the six heavy metals had a large correlation, Cd, Cu, Pb, Zn were greatly influenced by electroplating, smelting industrial production and the use of chemical fertilizers at agricultural activities. The results will provide a credible experimental basis for tracing the origin, migration, biological effects and comprehensive management of heavy metals in Taihu Lake.