The complex trade-offs and synergies among ecosystem services (ESs) in arid regions influence the stability and sustainable development of regional ecosystems. As a representative oasis-desert transition zone, the Kashgar region requires quantifying the key drivers and thresholds influencing ecosystem services, which is crucial for regional management. This study examines the spatio-temporal changes and interactions of five types of ES (grain production, water yield, soil retention, carbon storage, and habitat quality) and employs Restricted Cubic Splines to quantify the nonlinear changes and threshold effects of natural and social drivers. The results indicate the following: (1) During the period from 2000 to 2020, supply services (grain production) and regulatory services (water yield and soil retention) showed growth, while support services (carbon storage and habitat quality) declined slightly; (2) the synergistic effects of ecological services improved across the entire region, but trade-off effects emerged in certain local areas; and (3) the NDVI is the core natural factor driving the spatio-temporal differentiation of ESs. In 2020, when the NDVI exceeded 0.35, it had an adverse impact on habitat quality and carbon storage. Among social factors, water yield and habitat quality exhibit the highest threshold points with land use development intensity. An increase in land development intensity significantly impacts the trade-off and synergistic relationships among ESs, leading to local imbalances in ES resource supply and demand. These findings enhance our understanding of the nonlinear characteristics and potential mechanisms of ecosystems in arid regions, providing a scientific basis for ecosystem management in these areas.