Ecosystem management that attempts to maximize the production of one ecosystem service may result in substantial declines in the provision of other ecosystem services. For this reason, understanding the trade-offs and synergies of ecosystem services is of considerable significance to balance the characteristics of multiple ecosystem services and maximize the benefits of ecosystem services. The current situation is that there is insufficient researches on qualitative analysis and long time series of dynamic change among the trade-offs and synergies relationship. In addition, the selection of ecosystem services are inadequate. The Danjiangkou water source area is an important area of the South-to-North Water Diversion Project, and clarifying the temporal and spatial variation characteristics and relationships among ecosystem services can provide reference guidance for the smooth progress of the water transfer project in the middle route of the South to North Water Transfer project. At present, analysis of the relationships among ecosystem services in the Danjiangkou water source area is still insufficient. Given this situation, we studied the ecosystem service relationships of a long time series in the Danjiangkou water source area using different methods. First, we used the equivalent factor method to estimate the ecosystem service value. We then discuss the spatial-temporal difference and relationship of ecosystem services in six periods by correlation analysis and using an ecosystem services trade-off degree (ESTD) model. Correlation analysis has the advantage over long time series analysis. The ESTD model has the advantage of dynamic change analysis for short time periods. The results showed that during the period of 1990 to 1995, the value of ecosystem services in the Danjiangkou water source area showed a negative growth. However, the value of ecosystem services significantly improved from 1995 to 2015. The largest increase in ecosystem services occurred in water supply, and forest land provided the highest value of ecosystem services. Ecosystem service value increased from northeast to southwest. Correlation analysis showed that synergy is the dominate relationship among ecosystem services, and that there are few trade-offs in the Danjiangkou water source area. Since the Danjiangkou dam was heightened (after 2005), the relationship among ecosystem services in the water source area have changed. The trade-off relationships in the water source area increased among water supply, hydrological adjusting, and environment depuration, and trade-offs were reduced in other ecosystem services. Human disturbance is the most important factor that results in ecosystem service change.