Under the influence of climate warming and increased humidity on the Qinghai-Tibet Plateau, the river and lake systems in the source region of the Yangtze River have undergone significant changes. The Forel-Ule Index (FUI) quantifies water color changes to characterize the ecological status of water bodies. Understanding the spatio-temporal variations in lake water color and its driving factors behind these changes in this region is crucial for predicting future trends in the aquatic environment under changing climatic conditions. This study utilized Landsat and MODIS satellite images to obtain FUI indices for 264 lakes in the source region of the Yangtze River over the past 40 years. The analysis focused on the evolution of lake water color under varying meteorological and hydrological conditions, and the factors influencing these changes. The results indicated that from 1984 to 2023, a significant portion of barren land and grassland was transformed into water bodies, leading to a 1.96-fold increase in the number of lakes and a 1.65-fold increase in the average sediment transport modulus. The average FUI of lake water color decreased by two levels, with small lakes (＜5 km²) comprising 88.55% of the total lakes. These small lakes primarily exhibited yellowish hues (FUI＞9) due to the increased erosion of the basin, which had exposed a large number of shallow hot-melt lake basins. In contrast, large lakes (＞100 km²) showed a sustained trend towards blue hues (FUI＜6) as a result of rising water levels. This study enhanced our understanding of ecological and environmental changes in the lake systems of the Yangtze River source region over the past 40 years, and provided valuable insights for assessing the future evolution of the watersheds aquatic environment under climate change.