Since the outbreak of the 2019-nCoV, the whole society has participated collectively to resist the further spread of the epidemic. By sorting out the emergency measures for medical insurance and medical assistance during the outbreak of 2019-nCoV, major problems and potential risks in medical insurance and medical assistance were discovered. And then analyze the characteristics of modern epidemic risks and their special requirements for medical insurance, and Further improve the medical insurance and medical assistance mechanism for major diseases, which consist mainly of the fund-raising mechanism, object confirmation mechanism, fee payment mechanism, service provision mechanism, fee settlement mechanism, guarantee coordination mechanism and the supplementary security mechanism to provide countermeasures and suggestions for improving the medical insurance and medical assistance system for public health emergencies and major diseases, and provide a reference for improving the modernization level of the medical security governance system and governance capabilities.