The Chishui River Basin has been recognized as an important ecological security barrier in the upstream of the Yangtze River Basin. Research on the ecosystem service value of the Chishui River Basin under different future development scenarios is of great significance to carry out the environmental protection policies and the environmental protection measures. Therefore, Chishui River Basin has been selected as the research area and the FLUS (future land use simulation) model and InVEST (integrated valuation of ecosystem services and trade off) model were functioned to predict the ecosystem services, including water yield, soil conservation, and water purification, under three scenarios, such as natural development, environmental protection, and economic development in 2040. The high ecosystem services functions in all three scenarios are identified as the key protected areas. The results show as follows. There are significant changes in agriculture area and urban area under different scenarios, especially, the agriculture area under the economic development scenario has increased 510.55 km² and 1 475.76 km² compared to the natural development and environmental protection scenarios, respectively. In the environmental protection scenario, the areas with high water yield (> 700 mm) and high soil conservation function (>2 000 t/hm²) account for approximately 36.81% and 47.15% of the Chishui River basin area, respectively. The proportion of key protected areas for ecosystem services functions in the Zunyi City account for approximately 62.65%. The results of this study aim to provide certain support for identifying key protected areas in the Chishui River Basin and promoting the implementation of spatial refinement protection and management.