Public health emergencies not only bring great challenges to the conventional public health system, but also face some ethical dilemmas in the governance process. For example, the compulsory isolation measures affect the normal lives of some citizens, the normal medical treatment of non-epidemic patients may be constrained by complex governance environments, and the relationship between patient privacy protection and the public’s right to know needs to be deeply considered and balanced. To respond the ethical dilemmas in public health emergencies, it is necessary to explore more effective new ideas and methods under ethical concepts, combine with ethical needs in the governance of public health emergencies, comprehensively improve governance capabilities starting from the basic principles and behavioral standards of governance, with a view to providing more effective ethical support for the governance of public health emergencies.