This study examines the structural evolution of Knowledge Innovation Networks (KINs) and Technology Innovation Networks (TINs) across Chinese cities (2015–2024). Using SCI/SSCI co-authorship and prefecture-level patent data, we construct dual-layer networks and assess their resilience through metrics such as average clustering coefficient, path length, global efficiency, and largest-component ratio. Our framework clarifies how network structure, spatial proximity, and urban hierarchy jointly shape innovation dynamics and opportunity distribution. Three main findings emerge. First, KINs have moved toward polycentricity yet remain hierarchically rigid, with persistent core–periphery gaps despite improved connectivity in tier 2–4 cities. TINs show greater cross-tier adaptability, creating new innovation gateways while intensifying intra-tier polarization. Second, under simulated disruptions, KINs are vulnerable to targeted attacks and exhibit path-dependent degradation, whereas TINs maintain efficiency until a critical threshold, then collapse abruptly. Third, MRQAP analysis reveals that economic and geographic proximity facilitate collaboration in KIN but constrain linkages in TINs, with spatial proximity exerting a stronger influence on knowledge flows. These results demonstrate how innovation networks mediate urban–rural interactions, affect spatial inequality, and shape regional resilience. We argue for differentiated policies that strengthen core–periphery connectivity while mitigating proximity-induced lock-in, fostering more inclusive, resilient, and sustainable urban innovation systems.