The southern Tibetan Plateau (sTP) is an important source of global dust emissions and is also a region with a high concentration of human activities. Therefore, distinguishing climatic drivers of dust activity from anthropogenic influences is challenging. In this paper, we analyze a high-resolution aeolian sequence in the Yarlung Zangbo River basin on the sTP, which provides direct evidence of past dust accumulation. Quartz optically stimulated luminescence and radiocarbon dating indicate that this sequence accumulated during the early to middle Holocene, when human activity had a negligible influence on dust activity. We use grain size parameters including the sorting coefficient, residual grain size, grain size components determined by end-member modeling, and dust accumulation rate to reconstruct the history of natural dust storm activity. The results indicate a gradual decrease in dust storm activity from the early to middle Holocene. Combining modern meteorological data with climate simulations indicates that dust storm activity was co-regulated by the Qiangtang Plateau high (QPH) and the Indian summer monsoon (ISM). From the early to middle Holocene, with the gradual weakening of the QPH and ISM, both the near-surface wind intensity and the supply of dust materials decreased, which contributed to the decrease in dust storm activity. Overall, our findings provide new insights into the natural forcing mechanisms behind Holocene dust storm activity in this high-altitude region.