By 2050, a majority of the global population will reside in urban agglomerations. Intensifying natural hazards are posing serious challenges to populations within the urban agglomerations. Therefore, it is critical to evaluate the resilience of urban agglomerations to natural hazards. However, the urban resilience of China’s three major urban agglomerations, Beijing–Tianjin–Hebei (BTH), the Yangtze River Delta (YRD), and Guangdong–Hong Kong–Macao Greater Bay Area (GHMB), is not properly determined. To enhance the evaluation of comprehensive resilience in complex urban agglomerations and improve adaptability in the face of uncertain risks, this paper adopts the theory of complex adaptive systems to reveal the driving factors behind resilience. We developed a model for measuring disaster severity, exposure, bearing capacity, recoverability, and learnability. Furthermore, spatial autocorrelation analysis was employed to explore the distribution patterns of resilience and devise strategies for enhancement. The results indicate that the average urban resilience value of the three major urban agglomerations was 0.5061. The average urban resilience values for BTH, YRD, and GHMB are 0.5331, 0.5116, and 0.4612. We found BTH having the highest resilience level, followed by YRD and GHMB. Within BTH, the resilience level was the highest in the northern part of BTH, but the overall resilience of the southern cities should be improved by enhancing Shijiazhuang’s central role. We also found higher resilience level in northwest YRD than in southeast YRD due to lower population density and lower disaster exposure in northwest YRD. However, we found obscure spatial patterns of urban resilience within GHMB, i.e., higher urban resilience in east and west GHMB and lower urban resilience level in central GHMB. This study presents different urban resilience levels over three urban agglomerations, providing background information for urban planning and urban mitigation to natural disasters in a warming climate.