<p>Farmland soil of the Yarlung Zangpo River basin plays an important role in crop cultivation and highland barley is one of the staple foods of Qinghai-Tibet Plateau residents. This study assessed the current situation of heavy metal pollution in soil-highland barley system of farmland in the Yarlung Zangpo River basin. The pollution of As and Cr were found in farmland soil and highland barley, respectively. Soil heavy metals ranged from unpolluted to moderately polluted. The HI and TCR values for residents were above 1.00 and 1.00 × 10^–04, with As and Cr being the dominant contributors, respectively. Furthermore, identified non-carcinogenic risk and carcinogenic risk were also manifested by the result of Monte Carlo simulation. The source apportionment of soil heavy metals indicated that Cd primarily originated from industrial activities, Hg was the result of atmospheric deposition, As may stem from agricultural production, and other metals could be attributed to the natural factors. In conclusion, heavy metal pollution was found in soil-highland barley system of Yarlung Zangpo River basin and the pollution posed identified non-carcinogenic risk and carcinogenic risk to the adults and children. Among the studied metals, As and Cr should be the priority control objects.</p>