Abstract: At present, the diagnosis, treatment, and social security of rare diseases have attracts social attention. As an important part of the multi-level health insurance system in China, commercial health insurance plays an increasingly important role in the supplement to basic medical insurance. Moreover, recently, the benefits of new healthcare reform policies have provided much room and great opportunities for the application of commercial health insurance for rare disease.This paper presents current medical insurance for patients with rare diseases and discuss the necessity and feasibility of bringing rare diseases into the coverage of commercial health insurance, and analyzes the current application and the potential problems of rare disease insurance in the commercial health insurance. This article also gives suggestions to the policies to make full use of the positive role of commercial insurance for the completion of multi-level health insurance system for rare disease.