The Yangtze River Source Region (YRSR) is situated in a climate-sensitive zone, which is vulnerable to global climate change and human activities. The critical variations in its blue and green water resources have a profound impact on the management and sustainable development of water resources across the entire Yangtze River Basin. We investigated the spatiotemporal responses of blue and green water to climate warming-wetting trends and vegetation greening under land use changes, using the soil and water assessment tool (SWAT) model. Four combination scenarios considering climate warming-wetting and vegetation greening were established for quantitative analysis. The results indicate that precipitation and mean temperature in the YRSR exhibited significant upward trends from 1981 to 2020. During 1990-2020, 7,842.7 km2 of unused land was converted to grassland, while the leaf area index (LAI) showed a non-significant increasing trend. Under the combined effects of climate warming-wetting and vegetation greening, both blue and green water in the basin increased, with climate warming-wetting dominating the hydrological changes, contributing 70.24% and 96.28% to blue and green water variations, respectively. The warmer and wetter climate not only promoted vegetation greening but also indirectly enhanced water resources availability. Meanwhile, vegetation greening accelerated the conversion of blue water to green water, indicating that increased vegetation coverage optimized water resources distribution within the basin.