In the Hengduan Mountain region, soil erosion is the most serious ecological environmental problem. Understanding the impact mechanism of water yield and soil erosion is essential to optimize ecosystem management and improve ecosystem services. This study used the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) and Revised Universal Soil Loss Equation (RUSLE) models to separate the relative contributions of land use and climate change to water yield and soil erosion. The results revealed that: (1) Although soil and water conservation has been strengthened in the past 25 years, both water yield and soil erosion increased from 2010 to 2015 due to the conversion of woodland to grassland, which indicates that continuous benefits after the implementation of ecological restoration projects were not obtained; (2) Climate change played a decisive role in water yield and soil erosion changes in the Hengduan Mountain region from 1990 to 2015, and soil erosion was not only related to the amount of precipitation but also closely related to precipitation intensity; (3) The contribution of land use and climate change to water yield was 26.94% and 73.06%, while for soil erosion, the contribution of land use and climate change was 16.23% and 83.77%, respectively.