Coronavirus disease 2019 (COVID-19) both creates and complicates public health challenges. Yet, the pandemic also provides a unique lens for dissecting complex issues in global health that could benefit society in the long run. In this article, we discuss the underlying reasons that can help explain the divergent COVID-19 control outcomes between Beijing and Shanghai-two advanced metropolises that are similar in their municipal capacity, administrative capability and pandemic strategy. We hope insights from this investigation contribute to the development of disease prevention systems, such as context-specific and data-driven public health strategies that could yield optimal pandemic control outcomes with minimal unintended consequences, both amid and beyond COVID-19.