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The watershed boundaries in arid and semi-arid regions are critical zones where ecological vulnerability and socio-economic development are in severe conflict. The upper and middle reaches of the Yellow River basin are a typical example of this dilemma. Intensive land use and human developmental interventions in this region have severely disrupted the integrity and balance of the ecosystem. While spatially designated, networked conservation areas can effectively promote the integrity and balance of regional ecosystems, these areas may fail to capture dynamic changes in vulnerability. This study develops a “functional diagnosis-structural diagnosis-integrated optimization” framework. It integrates various scenarios to diagnose vulnerability under uncertainty and identifies bottlenecks in ecological networks. For functional diagnosis, the coupling of the sensitivity–resilience–pressure (SRP) model and the Ordered Weighted Averaging (OWA) algorithm accurately locates vulnerable areas within the regional ecosystem. In terms of structural diagnosis, the Morphological Spatial Pattern Analysis (MSPA), Minimum Cumulative Resistance model (MCR), and Circuit Theory are integrated to identify structural bottlenecks. The main findings of this study are as follows: (1) Functional Diagnosis: The coupling of SRP and OWA reveals the non-linear vulnerability responses to policy preferences and identifies areas that consistently exhibit functional vulnerability across different scenarios. (2) Structural Diagnosis: The circuit theory combined with MSPA and MCR analysis identifies 72 ecological pinch points. These bottlenecks represent the weakest structural nodes crucial for maintaining regional ecological robustness. (3) Coupled Delineation and Differentiated Restoration Strategies: High vulnerability areas identified by SRP and consistently vulnerable areas identified by OWA are combined to delineate four distinct ecological restoration units: Alpine Fragile Matrix Unit, Loess Hilly Soil Conservation Unit, Anthropogenic Pressure Pinch Point Unit, Key Structural Stepping Stone Unit. Differentiated ecological restoration strategies are proposed based on the varying sensitivity, resilience, and pressure characteristics of these units. The “functional-structural” coupled ecological vulnerability evaluation framework can precisely identify vulnerable areas. The delineated restoration units and their corresponding restoration strategies provide reference and supplementation for the protected areas system, offering transferable tools for enhancing regional ecological efficiency.