The long-term localization monitors on heavy metals during the past 10 years from 2001 to 2011(except 2004) were carried out in water of the five great lakes, including Lakes Taihu, Gehu, Hongze, Gaobaoshaobo and Luoma in Jiangsu Province. Nested data variance analysis was performed in order to compare the difference of heavy metals among the five above-mentioned lakes, and the Technique for Order Preference by Similarity to Ideal Solution(TOPSIS) method was employed to give a comprehensive assessment of heavy metals. The results indicated that concentrations of Pb, Cd, Hg and As were all very significantly different compared within the lakes except Cu. In addition, the concentrations of the five heavy metals at each monitor station were not significant. Concentrations of Pb, Cd and Hg were significant or very significantly different among years for each station. The TOPSIS results showed that the pollution of heavy metals in water of Lake Gaobaoshaobo was the smallest but was the greatest in Lake Luoma. For the remaining three lakes, the pollutions of heavy metals were almost at the same level.