As a key semi-arid subsystem for ecological protection in the Yellow River Basin, Fenhe River Basin is experiencing drastic changes in "social-ecological" structure, triggering cascading effects of morphological fragmentation and functional degradation. It is urgent to quantify coupling mechanism of ecosystem "structure-formfunction" (SFF) to break through the bottleneck of zonal restoration. This study integrated complex network analysis, mediation effect testing and multi-scale geographically weighted regression (MGWR) to reveal degradation characteristic and driving mechanisms of ecosystem services (ESs) from 2000 to 2020, and proposed differentiated zonal management strategies. The results showed that overall benefits of ESs presented a spatial pattern of "degradation in the central region and fluctuation along the northern and southern edges". Trade-offs dominated between habitat quality and soil conservation, as well as between habitat quality and annual water yield, while annual water yield and soil conservation demonstrated trade-offs in the northeast and northwest, and synergies prevailed in the middle and lower reaches. Driving mechanism evolved from "natural dominance human infiltration - synergistic driving", with elevation, cropland, and edge density serving as core driving factors in 2000, 2010, and 2020 respectively. Based on cascading effects, the study area was divided into six ecological zones, and differentiated strategies were put forward. The three-level policy loop of "driver factor identification - landscape process regulation - ecological response feedback" enriches the analytical framework within landscape sustainability science. Moreover, it provides novel perspectives and pathways for semi-arid basins to transition from single-element protection toward SFF collaborative governance.