Objective To establish a management scheme for the prevention and control of sudden respiratory infectious diseases on hospital ships and to evaluate its application. Methods The clinical practice, guidelines, expert consensus and systematic evaluation on the prevention and control of sudden respiratory infectious diseases at home and abroad were systematically retrieved. At the same time, the research team proposed a preliminary draft of the management scheme for the prevention and control of sudden respiratory infectious diseases on hospital ships by referring to the literatures on the management of major epidemics at home and abroad in recent years. After 2 rounds of discussion and amendment suggested by expert demonstration meetings, the management scheme for the prevention and control of sudden respiratory infectious diseases on hospital ships was finally formed, and preliminary verification was carried out in “Mission Harmony-2022”. Results The hospital ship management scheme for the prevention and control of sudden respiratory infectious diseases included 6 first-level items, 22 second-level items, and 40 third-level items (including 34 level-A recommended indicators and 6 level-B recommended indicators). The scheme was applied in “Mission Harmony-2022” and the task was successfully completed. Conclusion The management scheme for the prevention and control of sudden respiratory infectious diseases on hospital ships is systematic, comprehensive, rigorous, practical and scientific, and can provide a guiding reference for the rescue task of sudden respiratory infectious diseases on hospital ships.