In late February 2021, a round of indigenous novel coronavirus (referred to as COVID-19) infection emerged in Shanghai, making the COVID-19 outbreak shift from regular prevention and control to drastic pandemic prevention and control measures. According to the requirements of the Guidelines for the Organization and Implementation of Regional Novel Coronavirus Nucleic Acid Testing (Third Edition) issued by the National Health and Wellness Commission, medical institutions at all levels with nucleic acid testing capabilities rapidly carried out novel coronavirus nucleic acid testing, which put forward higher requirements for testing and prevention and control for the emergency conversion of non-designated admission hospitals to designated hospitals. As a clinical department with close contact with novel coronavirus testing specimens, the department of clinical laboratory has long working hours and high work intensity, as well as the potential risk of aerosol and contact transmission of clinical routine specimens and nucleic acid specimens, which requires more improvement from human resource planning, laboratory nucleic acid testing, laboratory infection prevention and control, medical material security, and staff psychological guidance. In this paper, we hope to combine the practice of emergency transformation work of the laboratory department in the northern hospital area of Ruijin Hospital, including personnel allocation, planning of testing items for clinical samples, and establishment of emergency nucleic acid testing, to carry out relevant work in a scientific, standardized and orderly manner, and provide our associate organizations with valuable experience in the coordination and management of emergency testing in the laboratory department in response to the novel coronavirus outbreak.