We generated a harmonized Chl-a dataset for the lakes in the Yunnan–Guizhou Plateau in China from 2013 to 2022 by the Landsat 8/9 and Sentinel-2A/B virtual constellation. Here, we shared the mean chlorophyll-a in nine major lakes in studied area. These dataset were aggregated from MSI- and OLI-derived Chl-a images and were subseted using the boundary of each lake. Data format is Geo-Tiff (*.tif) and zero values are INVALID values. More details on Chl-a retrievals can be found in: Z. Cao et al., "Harmonized Chlorophyll-a Retrievals in Inland Lakes From Landsat-8/9 and Sentinel 2A/B Virtual Constellation Through Machine Learning," in IEEE Transactions on Geoscience and Remote Sensing, vol. 60, pp. 1-16, 2022, Art no. 4209916, doi: 10.1109/TGRS.2022.3207345.