Ecosystem services-driven ecological networks are increasingly recognized as a strategic tool for guiding ecological restoration and conservation, particularly in ecologically fragile mountainous regions. However, most existing approaches remain static, often overlooking the spatiotemporal dynamics of service-driven networks in planning and management. This study proposed a framework for how to integrate multi-ecosystem services with network theory and assess network dynamics to delineate priority zones for restoration and targeted management in the Qilian Mountains. Results showed that the soil conservation, water supply, and carbon sequestration services in the study area generally improved from 2000 to 2020, and the identified key ecological patches and corridors predominantly concentrated in the eastern region. The complexity of ecosystem service-based networks fluctuated markedly over the study period, reaching its lowest point in 2010 (e.g., total corridor length dropped to 281.62 km) before partially recovering thereafter. Certain nodes (e.g., Patches 17 and 18) consistently served as the core hubs for connectivity, while others (e.g., Patches 1, 2, 8, and 24) showed high sensitivity to external disturbances. Based on these findings, targeted management recommendations were proposed for delineating priority restoration zones and core regulation areas in the Qilian Mountains protected area. This study provides a quantitative foundation for optimizing corridor restoration priorities and improving network resilience, offering methodological insights for conservation planning in arid regions globally.