The frequent occurrence of Public Health Emergencies of International Concern (PHEIC) has posed significant challenges to urban public health, economic, and social systems, exposing gaps in urban resilience. This study developed a dynamic urban resilience assessment framework against PHEIC based on the system dynamics method, integrating index analysis and the SEIR (susceptible–exposed–infectious–recovered) epidemiological model to investigate the interactions and dynamic evolution of urban subsystems in New York, Hong Kong, and Nanjing during the COVID-19 epidemic. The findings revealed significant differences in the response mechanisms and recovery capacities across subsystems. For example, the stringent lockdowns policy in New York curbed virus spread and heavily impacted economic activities; the “close to Dynamic zero of COVID-19” policy in Hong Kong demonstrated stronger resilience in balancing public health and economic recovery; the dynamic control measures in Nanjing China allowed for the rapid restoration of urban functions with minimal resilience fluctuations. Although strict control measures can effectively suppress disease spread, they can have profound economic and social impacts. More scientific strategies, such as those seen in Hong Kong and Nanjing, offer a more balanced approach to managing both epidemic control and urban function recovery, providing key insights for future PHEIC response strategies.