The COVID-19 pandemic, which lasted for three years, has had a great impact on the public health system, society and economy of cities, revealing the insufficiency of urban resilience under large-scale public health events (PHEs). Given that a city is a networked and multidimensional system with complex interactions, it is helpful to improve urban resilience under PHEs based on system thinking. Therefore, this paper proposes a dynamic and systematic urban resilience framework that incorporates four subsystems (governance, infrastructures, socioeconomy and energy-material flows). The composite index, system dynamics and epidemic simulation model are integrated into the framework to show the nonlinear relationships in the urban system and reflect the changing trend of urban resilience under PHEs. Then, urban resilience under different epidemic scenarios and response policy scenarios is calculated and discussed to provide some suggestions for decision-makers when faced with the trade-off between the control of PHEs and the maintenance of city operation. The paper concludes that control policies could be adjusted according to the characteristics of PHEs; strict control policies under a severe epidemic could lead to a significant decrease in urban resilience, while a more flexible control strategy can be adopted under a mild epidemic scenario to ensure the normal operation of urban functions. Moreover, the critical functions and impact factors of each subsystem are identified.