Rapid urbanization is fragmenting ecological spaces in megacities, threatening biodiversity and ecosystem services. Yet, it remains unclear whether, and under what conditions, urban ecological networks (ENs) can recover robustness once heavily disrupted. This study aims to (i) develop a dynamic assessment framework that couples network robustness and connectivity, and (ii) apply it to examine how ENs evolve under sustained urbanization and shifting policy regimes. Using multi-period data for Shenzhen, China (2000–2025), we simulate deliberate and random attacks on patches and corridors to derive data-driven thresholds that grade the importance of ecological elements, and integrate these with graph-based connectivity metrics to track changes in network structure and node centrality over time. Shenzhen’s EN exhibits a typical “fragmentation–reconfiguration–optimization” pathway, with a “rapid decline–deceleration–recovery” trajectory in robustness that closely aligns with the introduction of strict ecological control lines and subsequent restoration initiatives. The results show that targeted protection of residual core habitats, combined with strategic reconnection and infill greening in the urban interior, can reverse earlier losses in network robustness. The proposed robustness-informed framework provides operational guidance for prioritizing protection, restoration, and optimization of ecological space, and offers a transferable approach for adaptive EN planning in high-density tropical and subtropical megacities.