Abstract: The paper aims to master the pollution levels of heavy metals in the Yangtze River Basin. The authors selected Anhui and Jiangsu sections in the Yangtze River as sampling points, and collected 16 water samples in June 2016 to determine the contents of 6 heavy metals. The heavy metal contents in the water samples were determined by atomic absorption spectrophotometer. The results showed that: there were no residual Cd in the collected water samples, and the other heavy metals had varying degrees of residues; the residual mean value of Cr, Pb, Cu, Hg and As was 4.276, 1.866, 5.762, 0.016, 1.421 μg/L, respectively; as a whole, higher levels of heavy metals were found in Anqing and Jingjiang, followed by Nanjing and Tongling, while the pollution in Wuhu was the minimal; the Cr pollution in Jingjiang, Anqing and the Hg pollution in Tongling Site 1 reached tertiary level; secondary pollution area was mainly with Cu, Pb level in Tongling Site 1 also reached secondary pollution level, while the other elements’ pollution was insignificant. This study provides a basis for the effective control of heavy metal pollution in the lower reaches of the Yangtze River, and the realization of scientific management of water environment health risk, and has technical data support for quality and safety assessment of aquatic products.