The influence of paleoclimate in shaping current biodiversity pattern is widely acknowledged. However, it remains unclear how the upper paleo-range limit of trees, which dictated the habitat of endemic alpine species, affects the variability in endemic alpine species composition across space over the Tibetan Plateau. We integrated satellite-derived upper range limit of trees, dendrochronological data, and fossil pollen records with a paleoclimate dataset in a climate-driven predictive model to reconstruct the spatio-temporal upper range limit of trees at 100-year intervals since the Last Glacial Maximum. Our results show that trees distributed at the lowest elevations during the Last Glacial Maximum (~3426 m), and ascended to the highest elevations during the Holocene Climatic Optimum (~4187 m), a level ~180 m higher than the present-day (~4009 m). The temporal fluctuations in paleo-range limits of trees play a more important role than paleoclimate in shaping the current spatial pattern of beta-diversity of endemic flora, with regions witnessing higher fluctuations having lower beta-diversity. We therefore suggest that anthropogenic-caused climate change on decadal-to-centennial timescales could lead to higher fluctuations in range limits than orbitally-forced climate variability on centennial-to-millennium timescales, which consequently could cause spatial homogenization of endemic alpine species composition, threatening Tibetan endemic species pool.