Global climate change and human activities continue to threaten watershed ecosystems. The Jinsha River constitutes the upper reaches of the Yangtze River, so studying its ecosystem services (ES) is of great significance for maintaining ecological security and promoting ecological sustainability in the entire Yangtze River Basin. By using the integrated valuation of ecosystem services and trade-offs (InVEST) models and revised universal soil-loss equation (RUSLE) models, we evaluated five ecosystem services of water yield (WY), habitat quality (HQ), soil retention (SR), food supply (FS), and carbon storage (CS) provided by the Jinsha River Basin ecosystem from 2000 to 2020, as well as their spatial-temporal variations and driving factors. The results show three main features of this system. (1) From 2000 to 2020, each ecosystem service in the Jinsha River Basin exhibited different degrees of fluctuation, except for habitat quality, and each ecosystem service basically showed a spatial distribution pattern of high in the southeast and low in the northwest. (2) There were significant synergistic relationships between CS_SR_HQ and WY_SR_FS, and a significant trade-off between WY_CS. (3) The main driving factors of CS_SR_HQ were net primary productivity (NPP) and land-use type (LU), the main driving factors of WY_SR_FS were annual precipitation (PRE), LU, and rainfall erosivity (R), and the main driving factors of WY_CS varied considerably during the study period.