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In this study, we developed the tree-ring width chronology for the period of 1404 BCE to 2015 CE using Qilian juniper (Sabina przewalsku Kom.) trees collected from the Buerhanbuda Mts. in the southeastern Qaidam Basin (QB) near Nuomuhong Village, Qinghai Province. This is the first and longest chronology to date in this region. Based on the relationships between the tree-ring width chronology and climate data, the annual precipitation from previous July to current June (July-June) was reconstructed for the past 2917 years from 902 BCE to 2015 CE. This reconstruction accounted for 47.9% of the total variance in the actual July-June precipitation in the calibration period (1957-2015). The full reconstruction captured distinct wet and dry variability, and contained evidence of some low-frequency climate signals. We identified 13 wet and 12 dry periods, of which 1443-1503 CE and 1789-1836 CE were the two longest dry periods. General agreements in the low-frequency variations between the July-June precipitation and other moisture-sensitive records for the northeastern Tibetan Plateau (TP) suggested that the reconstruction in this study represented a regional signal. Spatial correlations with gridded precipitation data also indicated that the reconstructed July-June precipitation could adequately represent climate fluctuations over a large area of the northeastern TP. The new tree-ring width chronology and precipitation reconstruction are important for understanding natural climate change in the southeastern QB.