Millennium-aged trees are rare in natural forests. Here we present an 1184-year-long tree-ring width chronology from living juniper trees in the Biru area on the southeastern Tibetan Plateau. Growth-climate response analysis shows that the Biru chronology is significantly and positively correlated with late-spring (May-June) Standardized Precipitation Evaporation Index (SPEI) (r = 0.67, n = 53, p < 0.01). The tree-ring chronology explains 44.5% of the total variance of SPEI during the period AD 1957–2010. Reconstruction of May-June SPEI shows that there was a two-century-long megadrought during the late 13th to late 15th Centuries, and a seven-decade-long megadrought during AD 1630s to 1690s. Comparisons with other moisture records in the region suggest that the two-century megadrought identified in our reconstruction might be a widespread phenomenon most likely reflecting a stage of reduced Southwest Asian Summer Monsoon. Our results provide new evidence on the megadrought events on the Tibetan Plateau for the last millennium.