The major obstacle to optimizing the design of rare disease coverage is the fragmented decision-making process among medical services, pharmaceuticals, and medical insurance departments. There is an urgent need to realize data sharing and digital empowerment, as well as to adopt top-level design and systematic decision-making. It is also crucial to establish mechanisms, facilitated by digital intelligence, for sharing power and responsibilities, and assessing rewards and punishments. Furthermore, there is an urgent need to incorporate the theories of collaborative governance, digital governance, and the full life cycle into the entire process, which includes patient classification, diagnosis and treatment, medical assistance, medication protection, and health insurance fund management for rare diseases. This integration aims to provide theoretical reference for the effective linkage of medical services, pharmaceuticals, and medical insurance, and to improve the efficiency and equity of resource allocation in the public sector.