Over the past few decades, the Tibetan Plateau (TP) region has become gradually contaminated by persistent organic pollutants (POPs). The picture regarding POPs is clear in the central and southern parts of the TP; however, few observational campaigns have focused on the western TP. To clarify the concentrations, seasonal trends and source regions of POPs in the western TP, a first study of POPs in Muztagh Ata (westerly region) and a long-term (5 years) monitoring program in Ngari (transect region influenced by both the Indian monsoon and westerly climate) were conducted. Except for hexachlorobenzene (HCB) and polychlorinated biphenyls (PCBs), relatively low POP levels were observed in the western TP. In Muztagh Ata, dichlorodiphenyltrichloroethanes (DDTs) showed higher concentrations in winter and lower ones in summer, whereas at Ngari, higher DDTs and hexachlorocyclohexanes (HCHs) concentrations were observed in summer as compared with winter. Source diagnosis indicated that Xinjiang and central Asia were the main source regions for POPs in Muztagh Ata and that westerly winds play a key role in transporting POPs from central Asia. No correlation was found between the height of the atmospheric boundary layer and the concentrations of POPs over the TP.