Samples of surface water and sediment were collected in Taihu Lake and Nanjing section of Changjiang. Organochlorine compounds(OCCs) of samples were detected to investigate the characteristics and ecological risk of them in the lake and river. The concentrations of OCCs in water of Nanjing section of Changjiang were higher than those in Taihu Lake, but the concentrations of OCCs in sediments were higher in Taihu Lake. HCHs of Taihu sediments were relatively enriched, indicating the agricultural source of compounds. PCBs of Changjiang sediments were higher compared to Taihu sediments, denoting a obvious industrial source. Comparing with other compartments in China, HCHs of the study area were higher than most sediment of Chinese rivers, DDTs didn’t show high contents in sediments, PCBs was in relatively low levels. By contrast with the relevant sediment quality guidelines of these compounds, the ecological risk of OCCs in sediments were evaluated. The OCCs of sediments in Taihu Lake and Nanjing section of Changjiang didn’t show high ecological risk.