With the continuous accumulation of heavy metals (HMs), the threat of HMs to the ecological environment has attracted high attention worldwide. The Qu River basin is located in the upper reaches of the Yangtze River, the largest river in China, but its water quality spatio-temporal distribution characteristics, pollution sources and health risks of HMs are still kept unclear. In this work, based on 2160 samples containing 8 HMs including Hg, Pb, Se, As, Cu, Cd, Zn and Cr from 36 sampling sites, the health risks, water quality variation characteristics and pollution sources in the Qu River Basin were studied. The mean HMs concentration varied in different seasons, with higher content of Zn, Cd, Cu, Pb and Cr in dry season, higher As value in wet season. The water quality distribution pattern of Qu River Basin shows that the upstream is superior to that in the middle and downstream. Health risks of Cd and Cr were most pronounced during the study period. Moreover, Cd poses a greater potential health risk in dry season while Cr in the rainy season, respectively. Positive matrix factorization (PMF) receptor model indicated that industrial pollution (26.2 %), soil erosion (24.3 %), natural source (22.4 %), atmospheric deposition (21.0 %) and agricultural activities (6.1 %) are identified as the potentially sources of HMs of the surface waters in Qu River Basin. Therefore, from the perspective of health risks, the treatment and discharge monitoring of industrial wastewater and the restoration of soil contaminated by HMs should be further strengthened in the Qu River basin. This work will provide basic data for water quality improvement and resource utilization of Qu River Basin.