With the continuous refinement of China's rare disease prevention and treatment policies, the diagnosis and treatment capacity for rare diseases in China has been steadily improved; however, delayed diagnosis, inadequate transition of care, and poor continuity of long-term management remain common, particularly in pediatric rare diseases. Pediatric rare diseases often arise during critical developmental stages and exhibit age-dependent phenotypic evolution, such that diagnostic delays may lead to the missing of critical intervention windows. As the leading institution of the Hubei Provincial Rare Disease Medical Center and the Rare Disease Quality Control Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (hereinafter referred to as "Tongji Hospital") has established and implemented a rare disease discipline cluster model centered on platform convergence and specialty clustering. This model centers on the whole-life-cycle management needs of pediatric rare diseases, and constructs a systematic operational framework covering technical and data support, platform governance, specialized cluster operation, as well as regional and policy coordination. By summarizing the organizational pathway and practical effects of the rare disease discipline cluster construction at Tongji Hospital, this paper aims to provide a reference for general hospitals in promoting the development of rare disease diagnosis and treatment systems.