Rare diseases are mostly genetic disorders that often manifest in childhood, characterized by severe conditions, difficulties in diagnosis and treatment, and poor homogeneity in clinical management. Clinical research on rare diseases contributes to enhancing the diagnosis and treatment capabilities for rare diseases in China and promotes the development of rare disease medicine. Clinical research on rare diseases in China started relatively late, and there is currently no mature and comprehensive system for clinical research on rare diseases. This article analyzes the current state of clinical research on rare diseases in China, identifies existing problems and research difficulties, and proposes ideas and key measures for the construction of China’s clinical research system on rare diseases, aiming to provide opinions and suggestions for the construction of China’s clinical research system on rare diseases.