The prevention and treatment of rare diseases is an important public health issue in China. Rare diseases are characterized by diverse types, complex conditions, and heavy burdened to patients, leading to a series of issues in the urgent demand in prevention and treatment of rare diseases in terms of individuals′ health and the national responsibilities. Related legislation is an effective way to promote multi-disease prevention and treatment of rare diseases, and patients′ protection in multi-level. We tease out and analyze the legal system on national and local level related to rare diseases, and recommend the coping strategies and give suggestions to improve and optimize the legal system for the prevention and treatment of rare diseases from the three dimensions of completeness, normalization and feasibility of the legislation, hoping to improve the competence of China′s rare disease prevention and treatment and raise the level of protection for the patients.