Loss of alpine biodiversity under global warming poses a serious threat to biodiversity conservation and ecosystem services, yet few studies have addressed the discrepancies in alpine biodiversity across multiple altitude gradients over the millennia timescale. Here, our study selected three sites (Buqun Lake, Gongka Lake, and Shusong Co) at varying altitudes in the southeastern Tibet Plateau to reconstruct the evolution of vegetation communities during ~3500-0 cal BP using environmental metagenomics in lake sediment. The results suggest: 1) the biodiversity index increased rapidly at low altitude (~1500 m a.s.l) but decreased slowly at median altitude (3500 m a.s.l) and high altitude (4400 m a.s.l) during ~3500-2000 cal BP; 2) the biodiversity index at all three sites remained stable between 0.7 and 0.9 with slight fluctuations during ~2000-0 cal BP; 3) the biodiversity index at low altitude became more similar to those at median and high altitudes over the past millennium, despite differing community compositions among the sites at the three altitude gradients. Considering climate change and internal community interactions, our study primarily interprets that continuous regional warming during ~3500-2000 cal BP contributed to an increase in woody taxa with wide ecological niches (e.g., Salix, Populus, and Quercus) across multiple altitude gradients, further leading to a loss of diversity in alpine shrub-grassland. Meanwhile, these woody taxa with wide ecological niches were able to help resist further impacts from climate change after 2000 cal BP. Our study provides a new perspective on how internal community interactions can influence alpine biodiversity from a millennia-scale environmental metagenomics viewpoint.