The mobility and openness of smart cities characterize them as particularly complex networks, necessitating the resilience enhancement of smart city regions from a network structure perspective. Taking the Chengdu–Chongqing urban agglomeration as a case study, this research constructs economic, information, population, and technological intercity networks based on the complex network theory and gravity model to evaluate their spatial structure and resilience over five years. The main conclusions are as follows: (1) subnetworks exhibit a ‘core/periphery’ structure with a significant evolution trend, particularly the metropolitan area integration degree of capital cities has significantly improved; (2) the technology network is the most resilient but was the most affected by COVID-19, while the population and information networks are the least resilient, resulting from poor hierarchy, disassortativity, and agglomeration; (3) network resilience can be improved through system optimization and node enhancement. System optimization should focus more on improving the coordinated development of population, information, and technology networks due to their low synergistic level of resilience, while node optimization should adjust strategies according to the dominance, redundancy, and network role of nodes. This study provides a reference framework to assess the resilience of smart cities, and the assessment results and enhancement strategies can provide valuable regional planning information for resilience building in smart city regions.