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Biodiversity has attracted much attention recently due to its important relationships with ecosystem function under various global warming scenarios. However, an understanding of biodiversity mechanisms requires study over long time scales. Three high-resolution pollen records of Zoige Basin in the eastern Tibetan Plateau are used to reconstruct changes in vegetation diversity during the Holocene, allowing the mechanisms that drove the dynamic to be quantitatively explored. Rarefaction and Hill's indices are used to estimate the diversity richness and evenness based on pollen data. The results show that changes in palynological richness can be divided into five stages: an abnormal change from 10,500 to 9,000cal bp, an obvious increase from 9,000 to 6,500cal bp, a decreasing trend from 6,500 to 4,000cal bp, an increasing trend after 4,000cal bp until 1,500cal bp, and a highly fluctuating stage from 1,500cal bp to the present. Palynological evenness is relatively stable throughout the Holocene except for during a briefly elevated period from ca. 4,000 to 1,500cal bp. The result of Boosted Regression Tree analysis indicates that climate is the main driving factor and the effect of temperature is stronger than that of precipitation in the study region. However, during ca. 4,000-1,500cal bp, palynological diversity is primarily affected by vegetation structure, as shown by an increase in palynological evenness, which can in turn be explained by the climate threshold theory. This research provides a long-term, high-resolution reconstruction of palynological diversity which could be used to infer vegetation diversity change in the ecologically sensitive Tibetan Plateau. The results imply that vegetation diversity in the region may increase under global warming if human impacts are not considered.