Abstract: The heavy metals accumulated in the sediments is a potential threat to the urban river ecology. In August 2019, sediments were collected in Qingshui River, located in the main urban area of Chongqing. The content of heavy metals in the samples and the environmental indicators of adjacent surface water were monitored. The ecological risks and sources of heavy metals were evaluated by various statistical methods. The results showed that the average value of As, Cd, Cr, Cu, Hg, Ni, Pb and Zn in the sediments of the main stream of Qingshui River were 7.55±8.25, 0.238±0.056, 86.43±5.14, 78.21±18.22, 2.49±2.00, 33.86±5.29, 42.99±9.21 and 198.71±43.55 mg·kg^-1, respectively. According to the result of Geoaccumulation Index (Igeo) evaluation system, Hg reached the Severe Pollution Level, while Cu, Zn, Cd and Pb were at Slightly Polluted Level. The heavy metal content of sediments at most sites exceeded the current agricultural land soil pollution risk control standards, which indicated the dredged silt should be carefully used in agricultural land. The mean value of sediment Potential Ecological Risk Index (RI) was 1 984.54±1 515.92 and Hg contributed 90.78% for it, showing a great ecological risk of the sediments in Qingshui River. The exogenous sources of the heavy metals could be apportioned to the headwater and higher pH of the upstream surface water., which resulting in a gradual decrease trend of heavy metals (except As and Ni) from upstream to downstream. Due to the high gradient of mountainous rivers, the exogenous inputs of heavy metals at the headwater are able to affect the content of heavy metals in the sediments covering the entire upper and middle reaches. Principal component analysis and cluster analysis showed that Cr, Cu, Hg, Pb, and Zn in the sediments mainly originated from industrial point sources at the headwater, and there were three types of subdivisions derived from different types of industries. As and Ni mainly originated from sewage treatment station/urban non-point sources. Cd accumulation in the sediments were both significantly affected by the mentioned two sources.