In order to investigate the content of heavy metals in Lhasa River, water samples were collected from 16 sampling points in the middle and lower reaches of Lhasa River and the Duilonqu Tributary in July 2017. The concentrations of five heavy metals (As, Cd, Cu, Zn and Mn) were measured and the human health risks caused by these heavy metals via drinking water were evaluated. The results show that the concentrations of these five heavy metals in the water of the study area are as follows: Zn>Mn>Cu>As>Cd, which do not exceed the limit values specified in the Standards for Drinking Water Quality (GB 5749—2022). Moreover, the water quality of the study area also meets class I and Ⅱ standards (according to the Environmental Quality Standards for Surface Water (GB 3838—2002)). The high concentrations of As, Cu and Mn are primarily distributed in the lower reaches of Lhasa River and those of Zn are in the middle reaches. The results of health risk assessment show that the health risk of chemical carcinogen heavy metals is much greater than that of non carcinogen heavy metals. As is the leading chemical carcinogen heavy metal in Lhasa River, contributing 71.1% of the carcinogenic risk. The health risks caused by heavy metals via drinking water ingestion in Lhasa River are generally at an acceptable safety level; however, children are more susceptible than adults to the same health risk, which poses a greater threat to their health. Therefore, stricter regulatory measures are needed to manage children’s drinking water problems.