Abstract: It is a major public health task to promote the construction of modern disease prevention and control system in the prevention and control of the novel coronavirus pneumonia epidemic. In this study, we identified the current situation and challenges in the construction of disease prevention and control system in Shanghai, including the infrastructures, disciplines, human resources, information system, operational mechanism, and legalization. It is proposed that we should promote the construction of modern disease prevention and control system in Shanghai, which is aimed to improve the capacity in the disease prevention and control services, response to the major epidemics and public health emergencies, and scientific research in public health, in accordance with municipal functional orientation large-scale metropolitan public health security requirements in Shanghai. Moreover, we should promote policy-making, including upgrading infrastructures, facilitating discipline construction and scientific research innovation, optimizing development environment for human resources, accelerating comprehensive information construction, improving systems and mechanisms, and strengthening legal governance.