Unraveling the complex interactions among ecosystem services (ES) and their potential drivers in the context of large-scale climate change and ecological measures is crucial for enhancing ES multifunctionality (ESM) and ecological management. Compared with other regions, the gully region of the Loess Plateau suffers from severe soil erosion and fragile ecological environment, especially in the typical representative area of the Malian River Basin (MRB), which poses a huge challenge to multi-scale sustainable management. Based on the established ES analysis methods, this study investigated the MRB. Firstly, four typical ES, namely water yield (WY), water conservation (WC), soil conservation (SC), and carbon sequestration (CS), were mapped, and the cold and hot spots of ES maps were identified. Secondly, the mechanism of the interaction between ES and driving factors was clarified, and the trade-offs/synergies and combinations among ES were quantified. Finally, spatial planning and management strategies were formulated at the sub-basin scale. The results show that: (1) The spatial patterns of the four ES are stable, but their quantities change over time. From 1990 to 2020, the total amounts of WY and WC decreased by 28.47% and 24.90%, respectively, while SC increased by 16.48%. The hotspots of ESM are concentrated in the downstream area, while the coldspots are located upstream. (2) Precipitation is the main driving factor for WY, WC, and SC, with q values of 0.548, 0.697, and 0.030, respectively. NDVI has the strongest driving effect on CS (with a q value of 0.092). All factors do not have a constant impact on ES over time, and the interaction between two factors has a greater influence on ES. (3) ES exhibits a synergistic relationship at the global scale, while at the sub-basin scale, trade-offs and synergies coexist but undergo slight changes over time. WY-WC and WC-SC are dominated by synergy, while WY-SC is dominated by trade-offs. (4) Six ES bundles were identified, and their areas remained relatively stable during different periods. These findings can provide valuable insights for alleviating the degradation of ES in the gully regions of the Loess Plateau, coordinating the human-land relationship in the basin, and optimizing the zonal management of the ecosystem.