The outbreak of Omicron variant infectious disease not only affects Shanghai’s overall medical operation mode, but also generates enormous challenges and roadblocks of the implementation of treatment work, the accomplishment of the core medical systems and regimes, and the protection of patient safety to designated hospitals in Shanghai. As one of designated hospitals of Shanghai, the Baoshan Campus of Huashan Hospital has formed various multi-level management systems under the current circumstance, including the “hospital-level medical core management work system”， “specialized treatment guarantee-related work system” and “new crown-related special work system”. With the limited medical resources, Huashan Hospital regards flexible and intelligent implementation of the core system as an important task, and has built a series of management models. This paper has illustrated practical experience, and has provided reference for the purpose of maximizing the protection of patient’s safety and properly reacting during the outbreak of epidemic.