[Objective] The spatial-temporal changes and their causes of soil and water conservation services in the Sanjiangyuan region were explored in order to provide scientific evidence and data support for environmental protection measures and sustainable development in the area. [Methods] The soil and water conservation service capacity of the Sanjiangyuan region from 2000 to 2020 was quantitatively assessed using the net primary productivity (NPP) method and a driver factor analysis was performed using the optimal parameter geographical detector. [Results] ① From 2000 to 2020, land use in the Sanjiangyuan region underwent significant changes. The cultivated land, grassland, water bodies, and construction land continuously expanded, whereas the forest land and unused land areas decreased. The region is mainly dominated by grassland, followed by water bodies and forest land. Over the 20 year period, vegetation coverage showed a generally stable increasing trend with an overall spatial distribution pattern of “higher in the east and lower in the west.” ② From 2000 to 2020, the soil and water conservation service capacity index followed an N-shaped trend, but overall, the index had an increasing trend over the time period with a growth rate of 26.13%, indicating a significant improvement in the soil and water conservation service capacity. The distribution of the soil and water conservation service capacity was relatively consistent, displaying an overall “higher in the east and lower in the west” spatial distribution pattern. Throughout this period, the gravity center in the Sanjiangyuan region remained in the western part of Maqin County, with increased soil and water conservation capacity towards the northwest and multidirectional extension. This result indicated the engineering projects that had been implemented had significantly improved soil and water conservation service capacity. ③ Factors, such as vegetation coverage, GDP per unit area, and grazing intensity, had considerable impacts on soil and water conservation services and the interactions between vegetation coverage and GDP per unit area, average annual rainfall, grazing intensity, and other factors explained a considerable proportion of the change. [Conclusion] It is essential to continue implementing natural forest protection projects and promote forest conservation and restoration to significantly enhance the forest stock. Furthermore, measures, such as rational grazing, construction of artificial grasslands, fencing, and reseeding, should be adopted to protect ecosystems.