At present, there are some problems in the post-diagnosis service of rare diseases, such as immature service path, imperfect health supervision and discontinuous to post-diagnosis data flows. How to properly solve these problems and find a way to promote the post-diagnosis service of rare diseases is the focus now. Based on the actual situation of diagnosis and treatment of patients with rare diseases in West China Hospital of Sichuan University and literature. This paper finds that making full use of the method of intelligent continuous management, establishing a continuous health management system, and integrating rare disease data information through intelligent health management platform and internet medical treatment can alleviate the shortage of medical resources and solve the dilemma of post-diagnosis service of rare diseases. At the same time, this paper analyzes the dilemma of post-diagnosis services of rare diseases and the feasible countermeasures of intelligent medical assistance management, and explores the management of rare diseases led by tertiary hospitals and joint built by medical units of the hospital alliance, in response to the national graded diagnosis and treatment policy, so as to provide all-round health protection for patients with rare diseases for reference and learning.