Abstract: Congenital disorders are a significant cause of infant and child mortality and congenital disabilities, and implementing comprehensive prevention and treatment strategies for congenital disorders has become a widely adopted approach by the international community. However, a number of ethical issues have also arisen in the implementation of prevention efforts. The importance and urgency of thoroughly analyzing the ethical risks involved and promoting the establishment and implementation of ethical standards in the process of prevention and treatment of congenital disorders have been highly concerned by clinicians in maternal and child health and experts in related research fields. This article analyzes the main ethical dilemmas in the prevention and treatment of congenital disorders and proposes ethical principles that can currently be used in the practice of three-level prevention of congenital disorders, so as to promote the ethical governance of prevention and treatment efforts in China.