While large-scale vegetation restoration has significantly greened the Yellow River Basin (YRB), it remains unclear whether this quantitative 'greening' translates into an improvement of habitat integrity, particularly regarding the potential trade-offs between carbon sequestration and habitat quality. Based on multi-source remote sensing data (LULC, NDVI, DEM, soil and meteorological interpolation data), this study assessed water conservation (WC), soil conservation (SC), carbon storage (CS), and habitat quality (HQ) from 2000 to 2020 using the InVEST model. Geographically Weighted Regression (GWR) and Geodetector (GD) were applied to spatially disentangle ES trade-offs and synergies and to identify their driving mechanisms. The results showed that while CS increased steadily (from 17.167 & times; 1011 t to 17.266 & times; 1011 t), HQ and WC exhibited declining trends. Spatially, ES hotspots were concentrated in the Bayan Har-Animaqing Mountains, while WC cold spots migrated northward toward the Mu Us Sandy Land by 2020. The spatial heterogeneity of these ESs was significantly associated with the coupled effects of socioeconomic and natural factors, notably the interactions between climatic variables and land-use area. Although the synergy between water and SC strengthened, the synergies involving CS-specifically CS-WC and CS-HQ-weakened significantly. These findings suggest that while vegetation expansion is a dominant factor, its impact on ES trade-offs is moderated by regional biophysical constraints. Future ecological strategies in the YRB must shift from simple vegetation expansion to a more nuanced approach that balances carbon sequestration with biodiversity and habitat integrity.