A total of 98 monitoring sites were set up in the Lake Taihu Basin and water and sediment samples were collected routinely from these sites during the period from November 2012 to August 2013 for analysis of heavy metals (Cr, Cu, Zn, As, Cd, Pb and Hg) with the Inductively Coupled Plasma-Mass Spectromtry (ICP-MS) and a Direct Mercury Analyzer, to explore content distribution characteristics of the heavy metals and status quo of heavy metals pollution of the region. Results show that: the seven heavy metals (Cr, Cu, Zn, As, Cd, Pb and Hg) in the surface water did not exceed the criteria set in the National Environmental Quality Standards for Surface Water in content, being 0.88, 3.21, 10.96, 3.29, 0.019, 0.07 and 0.021 μg·L-1, on average, while the content of Cr, Cu, Zn, Cd and Pb in the sediment was 102.32, 65.24, 185.64, 0.93 and 45.88 mg·kg-1, on average, all exceeding the criteria set in the standard, especially the content of Cd, being 4.7 times as high as the criterion in the standard. However, the content of As and Hg was only 9.87 and 0.107 mg·kg-1 on average, respectively, or 65.8% and 71.3% of their respective criterion in the standard. Contents of the seven heavy metals in the surface water and sediment varied significantly in temporal and spatial distribution. The concentrations of Cr and Cu in the surface water were higher during the normal water seasons than during the high or low water seasons, and the concentrations of Zn and As the highest during the high water season, whereas the concentrations of Cd, Pb and Hg relatively unchanged throughout all the three seasons. Cr, Cu, Zn, As, Cd and Hg were the highest in concentration in the Canal water system area, the lowest in the water body of Shaoxi and moderate in the water body of Lake Taihu. In the sediments, the concentrations of Cr and Cu were higher during the normal water season than during the high or low water seasons; the concentrations of Zn, Cd and Hg were the highest during the high water seasons and the lowest during the low water season; and the concentrations of As and Hg were the highest during the low water seasons in the sediments of the Canal water system and the effluent system, the concentrations of Cr, Cu and Pb were significantly higher than the criteria in the standard, while in the sediments of the other water system, their concentrations were lower or approximate to the criteria in the standard. Zn content in the sediments was the highest in the effluent water system and the Canal water system, while Cd content was in the Yili water system and the Taihu Lake water system. In the sediments of the Taihu Lake Basin, the 7 heavy metals followed a decreasing order of Cd > Hg > Cu > As > Pb > Cr > Zn as potential ecological risk factor, among which Cd was the paramount one, reaching the heavy level in ecological hazard degree. Of the heavy metals, the ecological risk index in the Yixi River water system was rated as heavy ecological hazard, being 278.13, while the indices in the other areas as moderate ecological hazard.