Heavy metals are toxic, persistent and non-degradable. After sedimentation and adsorption, they accumulate in water sediments. The aim of this study was to understand the heavy metal pollution of Qinjiang River sediments on the ecological environment and apportioning sources. The mean total concentrations of Mn, Zn, Cr, Cu, and Pb are 3.14, 2.33, 1.39, 5.79, and 1.33 times higher than the background values, respectively, except for the Co, Ni, and Cd, which are lower than the background values; Fe, Co, Ni, Cd, Cr, Cu, and Pb are all primarily in the residual state, while Mn and Zn are primarily in the acid-soluble and oxidizable states, respectively. Igeo, RI, SQGs and RAC together indicate that the pollution status and ecological risk of heavy metals in Qinjiang River sediments are generally moderate; among them, Fe, Co, Ni, Cd, Cr, and Pb are not harmful to the ecological environment of the Qinjiang River. Cu is not readily released because of its higher residual composition, depicting that Cu is less harmful to the ecological environment. Mn and Zn, as the primary pollution factors of the Qinjiang River, are harmful to the ecological environment. This heavy metal pollution in surface sediments of the Qinjiang River primarily comes from manganese and zinc ore mining. Manganese carbonate and its weathered secondary manganese oxide are frequently associated with a significant amount of residual copper and Cd, as a higher pH is suitable for the deposition and enrichment of these heavy metals. Lead-zinc ore and its weathering products form organic compounds with residual Fe, Co, Cr, and Ni, and their content is related to salinity. The risk assessment results of heavy metals in sediments provide an important theoretical basis for the prevention and control of heavy metal pollution in Qinjiang River.