We have now entered a critical period for prevention and control, since the outbreak of the Coronavirus Disease 2019 (COVID-19) in Wuhan in December 2019. As an important component of disease diagnosis and treatment, hospitals have great significance in controlling the spread of the virus by responding rationally and carrying out hospital prevention and control during the epidemic. This paper analyzes the management methods, experience and thinking of The First Affiliated Hospital with Nanjing Medical University to deal with the epidemic during the epidemic which provide a reference for the medical institutions to overcome the Coronavirus Disease 2019.