Small lakes (areas between 0.01 km2and 1 km2) on the Qinghai–Tibet Plateau (QTP) are prone to fluctuations in number and area, with serious implications for the surface water storage and water and carbon cycles of this fragile environment. However, there are no detailed long-term datasets of the small lakes of the QTP. Therefore, the intra-annual changes of small lakes in the Qilian Mountains region (QMR) in the northeastern part of the QTP were investigated. The small lake water bodies (SLWB) in the QMR were extracted by improving existing commonly used waterbody extraction algorithms. Using the Google Earth Engine platform and 13,297 Landsat TM/ETM + /OLI images, the SLWB of the QMR were extracted from 1987 to 2020 applying the improved algorithm, cross-validation and manual corrections. The reliability, uncertainty and limitations of the improved algorithm were discussed. An intra-annual small lake dataset for QMR (QMR-SLD) from 1987 to 2020 was released, containing eight attributes: code, perimeter (km), area (km2), latitude and longitude, elevation (m), area error, relative error (%), and subregion.