The Selinco Basin, a sub-basin with the highest concentration of lakes in the endorheic region of the Tibetan Plateau, plays a crucial role in determining the stability of the regional ecological environment. Understanding the spatial distribution and spatiotemporal changes in its ecosystem functions, as well as the complex trade-offs and synergies among key ecosystem services, is essential for developing science-based conservation strategies and sustainable management practices. By integrating the InVEST model with spatial statistics and geodetector analyses, we systematically assessed land use patterns and four key ecosystem services—water yield, soil retention, carbon sequestration, and habitat quality—over the past two decades (2000–2020). Furthermore, we conducted a multidimensional analysis to quantify the factors driving these changes. The results indicate that: From 2000 to 2020, the water area within the basin experienced the most significant change, increasing by approximately 147.09 km2.The annual average values for water yield, soil retention, carbon sequestration and habitat quality in the Selinco Basin are 56.23 mm, 218.78 t·km?2, 132.01 g C·m?2 and 0.71, respectively. Water yield decreases from northeast to southwest; soil retention is lower in the central region and higher on the sides; carbon sequestration decreases from southwest to northeast; and habitat quality shows minimal spatial heterogeneity. Over the past 20 years, water yield decreased slightly, soil retention and carbon sequestration showed a slight increasing trend, with area of increasing trend accounting for 28.33%—58.21% of the Selinco Basin. Habitat quality was relatively stable, with 87.93% of the area remaining unchanged. There was a trade-off relationship between water yield and the other three ecosystem services, particularly evident in the northeast region. Additionally, there was a synergistic relationship among soil retention, carbon sequestration, and habitat quality. The spatial distribution of ecosystem services is mainly influenced by the uneven distribution of natural factors like temperature, precipitation, and vegetation. Temperature and precipitation best explain water yield, while elevation is the most significant factor for soil retention and habitat quality. NDVI has the strongest explanatory power for carbon sequestration. This study provides data and theoretical support for ecological protection and management in the Selinco Basin, and contribute to the construction of ecological protection in the ecological barriers on the Tibetan Plateau.