[Objective] Scientifically estimate the value of ecosystem services in the Sanjiangyuan region to provide a scientific basis for understanding the ecological asset reserves and ecological security safeguards of the watershed. [Methods] Using the improved equivalent factor method, substitute engineering method, and substitute cost method, we scientifically assessed the total value of ecosystem services and the value of individual ecological service functions in the Sanjiangyuan region. By employing remote sensing and spatial statistical analysis techniques, we examined the spatial distribution characteristics of ecosystem service values in this region and identified its core functional zones. [Results] ① The total value of ecosystem services in the Sanjiangyuan region amounts to 246.485 billion yuan. Among these, water conservation services hold the highest value at 93.401 billion yuan, accounting for 38% of the total and consistent with the region’s designation as China’s ‘water tower.’ Climate regulation and soil conservation follow, comprising 33% of the total value. Habitat protection and landscape aesthetics contribute 21% of the total value. Air purification services showed the lowest value, accounting for only 8% of the total. ② The values of water conservation, soil retention, habitat protection, and landscape aesthetics exhibited a ‘higher in the north, lower in the south’ pattern, while climate regulation and air purification values demonstrated an ‘higher in the east, lower in the west’ distribution characteristic. [Conclusion] Yushu Xizang Autonomous Prefecture and Guoluo Xizang Autonomous Prefecture serve as vital climate regulation zones and soil conservation areas. Efforts to advance forest and grassland ecological protection and restoration should be sustained, establishing a comprehensive system for soil and water erosion control to continuously enhance soil retention capacity. Haixi Mongol and Xizang Autonomous Prefecture, Yushu Xizang Autonomous Prefecture, and Guoluo Xizang Autonomous Prefecture are vital water conservation and recharge areas. Efforts should be intensified to protect wetland water bodies and reduce the risk of contamination. Different river basins should strengthen coordinated governance and scientifically plan landuse.