Exploring the water yield and soil conservation in the Three-River-Source region is of great significance for evaluating both the ecological stability of the Qinghai-Tibet Plateau, Yellow River basin, Yangtze River basin and Lancang River basin and the sustainable development of human society. The data sources for this study were land use/cover data from four phases (2000, 2005, 2010 and 2015), daily precipitation and temperature datasets, and the 1:1000000 Chinese soil database. These data were combined with vector data, such as data on settlements, roads, and rivers, along with population, economic raster datasets and CCSM4 common climate model prediction results. The Three-River-Source region was taken as the study area, and four land use/cover development scenarios and two climate change scenarios were designed based on the FLUS model and the downscaling correction method. The InVEST model was used to quantitatively simulate the water yield and soil erosion under different scenarios in the study area in 2030. The results showed the following: (1) Under different land use/cover development scenarios, grassland remained the dominant land use/cover type in the Three-River-Source region, and the area ratio was always greater than 67%. (2) Under the RCP4.5 climate scenario, the annual water yield and soil erosion increased by more than 7% and 3.9%, respectively. Under the RCP8.5 climate scenario, the annual water yield and soil erosion decreased by more than 3.3% and 1.3%, respectively. (3) Climate change played a leading role in the changes in water yield and soil erosion. Climate change contributed as much as 89.97%–98.00% to the change in water yield and 60.49%–95.64% to the change in the soil erosion modulus. However, the contribution of land use/cover changes to the change in regional water yield was only 2.00%–10.03%, and the contribution of the soil erosion modulus change was 4.36%–39.91%. Therefore, the land use development strategy in the Three-River-Source region should comprehensively consider issues such as regional development, the input of returning farmland to forest and grassland, and the resulting ecological benefits.