Due to the influence of the Indian monsoon system, air mass transport in and to the Tibetan Plateau shows obvious seasonality. In order to assess the responses of atmospheric concentrations of persistent organic pollutants (POPs) to the Indian Monsoon fluctuation patterns, a three year air monitoring program (2008–2011) was conducted in an observation station close to the Yarlung Tsangpo Grand Canyon, southeastern Tibetan Plateau. The air concentrations of polychlorinated biphenyls (PCBs) and hexachlorocyclohexanes (HCHs) are generally comparable to those of other remote regions, whereas the concentrations of DDTs are much higher than reported for the polar regions, the North American Rocky Mountains, and the European Alps. The concentrations of DDTs and PCBs were strongly linked to the cyclic patterns of the Indian monsoon, displaying higher values in the monsoon season (May–September) and lower values in the nonmonsoon season (November–March). A “bimodal” pattern was observed for α- and γ-HCH, with higher concentrations in spring and autumn and lower concentrations in the summer (monsoon season). Rain scavenging in the monsoon season likely resulted in the lower HCH concentrations in the atmosphere. This paper sheds lights on the role the Indian monsoon plays on the atmospheric transport of POPs to the Tibetan Plateau.