For the surface sediment samples of Taihu Lake in 2010, the eight physicochemical indices of pH, temperature, Eh, water content, porosity, grain size, total phosphorus, and Loss-on-ignition were measured and analyzed, along with the contents of nine heavy metals:Cu, Zn, Ni, Cr, Pb, Ba, Mn, Co, and V. The order of magnitudes of heavy metal content of surface sediments in Taihu Lake was:Mn>Ba>Zn>Cr>V>Ni>Pb>Cu>Co. This suggested that the contents of the nine heavy metals were beyond the background value, which had a close connection to the geology of the Taihu Lake Basin and were influenced by human activity to varying degrees. The clustering analysis and the spatial distribution of the heavy metals revealed that the concentrations of heavy metals in the North and South Taihu Lake sections decreased from the lake shore to the lake center, the concentrations of heavy metals in the West Taihu Lake section increased from the lake shore to the lake center, and the distribution of heavy metals in the center of the lake remained relatively uniform. According to the correlation study, the metal elements were positively correlated with one another to varying degrees, indicating that they originate from the same source of pollution. According to the PCA and PMF analyses, there were some different sources of heavy metals in Taihu Lake, in which the transportation and industrial complex source were the most important sources, the diagenesis was the second major source, and agriculture was the third major source. Furthermore, the heavy metal pollution was evaluated using the geoaccumulation and the potential ecological risk indices. This offers a solid theoretical backing for the future management of heavy metal pollution in Taihu Lake.