The difficulties in diagnosing rare diseases, seeking medical treatment, and low drug accessibility have become a public health governance challenge in China and even globally. The fragmentation of China’s rare disease prevention and protection system is evident, and relevant policies urgently require legal authorization and solidification.Research and development of rare disease drugs lack effective legal and policy incentives. Special legislation is an effective way to solve the dilemma of rare disease prevention and protection. Promoting special legislation for rare diseases in China at present is an inherent requirement for achieving social justice and protecting the right to health of patients. There is a broad social consensus and mature experience outside the region for reference. The functional positioning of special legislation for the prevention and protection of rare diseases should be clarified, a reasonable value orientation for differential treatment should be established, and the construction of special legislation for rare diseases should be promoted through adhering to the idea of central coordination and local pilot parallel promotion.