Abstract: The Three-River Headwaters (TRH) region (89°45'–102°23'E, 31°39'–36°12'N), located in the southern part of Qinghai Province in China and on the central-eastern part of the Tibetan Plateau, is an important water conservation area and the key area for eco-environment protection in China. The glaciers located in this region are important water supply for the Yangtze, Yellow, and Mekong rivers. Based on ASTER GDEM and Landsat TM/ OLI images acquired in 2000s, 2010s, and 2019, the outlines of individual glaciers in the TRH region were obtained by using the band ratio method combined with manual revision. Meanwhile, some properties of each glacier including name, area, elevation, mountain, drainage basin and remote sensing imagery adopted were provided. This dataset is composed of the vectorized data of glacier outlines in 2000s, 2010s and 2019 and an excel table containing the change information of individual glacier area in 2000—2019, which can be used as the basic data for research on glacier changes, the assessment of glacial water resources in the TRH region.