Polycyclic Aromatic Hydrocarbons (PAHs) and Polychlorinated Biphenyls (PCBs) are significant components of persistent organic pollutants (POPs) and pose a threat to both ecosystems and human health. To explore their spatial distribution, origins, and risk assessment, we collected 25 glacial meltwater and downstream river water samples in the eastern Tibetan Plateau (including the Qilian Mountains in the northeast) during the summer of 2022 (June-July). Our results showed that ∑PAHs and ∑PCBs were present in a wide range from ND-1380 ng/L and ND-1421 ng/L, respectively. Compared to other studies worldwide, the ∑PAHs and ∑PCBs in the Hengduan Mountains were at high levels. The PAHs and PCBs mainly consisted of low-molecular-weight homologs, including Ace, Flu, Phe, and PCB52. Phe was the primary component of PAHs. Glacial meltwater samples generally exhibited low concentration of PAHs and PCB52, whereas downstream river water samples typically showed high concentration of PAHs and PCB52. We attributed this characteristic to the influence of pollutants physicochemical properties, altitude effect, long-range transport (LRT), and local environmental conditions. In the eastern Tibetan Plateau glacier basin (especially in the Hailuogou watersheds), the concentration of PAHs and PCB52 in runoff generally increased with decreasing elevation. We believe that the primary factor affecting the concentration of PAHs and PCB52 in the region is the difference in local human activity inputs from various altitudes. The composition characteristics of PAHs and PCBs suggested that incomplete coal combustion and coking discharge mainly caused PAHs, while the combustion of coal and charcoal and the release of capacitors primarily caused PCBs. We assessed the carcinogenic risk of PAHs and PCBs in the glacier basin of the TP and found that the potential threat of PAHs was stronger than that of PCBs. Overall, this study provides new insights into the ecological security of water resources in eastern Tibetan Plateau. It is significant for controlling PAHs and PCBs emissions, assessing the ecological environment of the glacier watershed, and regional human health.