Lake Taihu is the third-largest lake in China, which is located at the junction of Shanghai City, Jiangsu Province and Zhejiang Province. Lake Taihu and Taihu Basin play a crucial role in the implementation of the national strategy of the integrated development of the Yangtze River Delta region. To characterize the pollution characteristics of heavy metals in shallow sediments in the coastal area of Lake Taihu, the monitoring test data for heavy metals of 230 sediment samples at 0-10 cm depth, 159 sediment samples at 10-20 cm depth, and 115 sediment samples at 20-30 cm depth were collected which were from the investigation project of polluted sediments in Lake Taihu in the year of 2018. The contents of eight heavy metal elements (Hg, Cd, As, Pb, Cu, Zn, Cr and Ni) in the samples which in Meiliang Bay, Zhushan Bay, Western Coastal Area of Lake Taihu, Southern Coastal Area of Lake Taihu, East Lake Taihu and Gonghu Bay were analyzed. The potential ecological risk index method and spatial interpolation analysis method were applied to evaluate the ecological risk of heavy metal pollution in sediments, and the sources of heavy metals in sediments were preliminarily analyzed. The results showed that the distribution of heavy metals in shallow sediments had evident spatial heterogeneity. The heavy metals' contents in Zhushan Bay, Western Coastal Area of Lake Taihu, Gonghu Bay and Meiliang Bay were higher than those in the Southern Coastal Area of Lake Taihu and Eastern Lake Taihu. The contents of Cd, Pb, Cu, Zn and Ni in each lake area, the contents of Hg, As and Cr in Zhushan Bay, the contents of As and Cr in Gonghu Bay, the content of As in the Southern Coastal Area of Lake Taihu, the content of Cr in Meiliang Bay were higher than the background value. The heavy metals contents in sediments in different depths of 0-30 cm had a rise from its bottom to its surface. The potential ecological risk assessment results presented that the seriously polluted area of heavy metals in sediments at 0-30 cm depth which heavy metals ecological risk index RI ≥ 300 were mainly distributed in the central part of the Western Coastal Area of Lake Taihu (the nearshore side from Jiaodu River to Wuxi River), the northern part of Zhushan Bay, the northern part of Gonghu Bay. The distribution area was 104.54 km², 10.80 m² and 6.89 m² respectively, with a total area of 122.23 km². Cd and Hg were the main heavy metal ecological risk contributors with strong toxicity. The Western Coastal Area of Lake Taihu and Gonghu Bay were mainly polluted by Cd, Zhushan Bay was mainly polluted by Cd and Hg. The Cd pollution in the Western Coastal Area of Lake Taihu was the most serious. The heavy metals source analysis results demonstrated that the Zn, Cu, Cr, Ni, Hg, Pb and As in shallow sediments in the coastal area of Lake Taihu have similar sources, which may mainly come from industrial pollution. Moreover, the Cd may come from agricultural pollution. The research results can provide references and basic data supports for the prevention and control of heavy metal pollution in the sediments of Lake Taihu.