The Tibetan Plateau, known as the third pole of the Earth, is a region susceptible to climate change. With little human disturbance, lake storage changes serve as a unique indicator of climate change, but comprehensive lake area and volume data are rare in the region, especially for the lakes with an area less than 10 km2 which are the most sensitive to environmental changes. In this dataset, we completed a census of annual lake area and volume change for 976 lakes larger than 1 km2 in the endorheic basin of the Tibetan Plateau (EBTP) during 1989-2019 using Landsat imagery and digital terrain models. This dataset contains the lake extents shapefile containing the annual area and relative volume data from 1989 to 2019 for each lake. Besides, the lake seeds we used to calculate the relative lake volume are also published.