With the implementation of the Great Western Development Strategy, the ecological risks associated with social and economic development have attracted the attention of ecologists and government departments. As an important base for maintaining plateau biodiversity, Lhasa River Basin is also an important ecological safety barrier zone for China and East Asia more broadly. To effectively control the ecological risks in the process of urbanizing Lhasa River Basin, this study identified the source of risks, selected risk receptors, and used a relative risk model to calculate the risk level in each research unit. The results show that the Chengguan District has the highest ecological risk level, with the primary risk coming from urban expansion and tourism; and Dangxiong County has the lowest level of ecological risk, with the risk coming from livestock husbandry. The primary source of risk in Linzhou County, Qushui County, Dazi County, Dulongdeqing District, and Mozhugongka County is agricultural pollution. The risk value for water and wetland is significantly higher than that of the other habitats. The spatial distribution of risk value is generally higher in the south of Lhasa River Basin, and the risk level decreases gradually around the Chengguan District.