Objective: The paper attempts to understand the allocation of rare diseases negotiation drugs in various provinces (cities), and analyze the accessibility and implementation of negotiation drug policies to provide theoretical basis for policy improvement. Methods: The paper collects the allocation data of 20 orphan drugs in national medical insurance service platform, and analyzes the distribution of these drugs in hospitals and pharmacies. Results: Hospitals and pharmacies in Guangdong, Jiangsu, Zhejiang, Shandong and Henan supply these orphan drugs more than other provinces (cities), with 20 orphan drugs available. Hospitals and pharmacies in Tibet, Hainan, Ningxia, Guangxi and Qinghai supply relatively less orphan drugs, and the number of unavailable drugs is 14, 8, 8, 6 and 5 respectively. From the perspective of drug dosage forms, oral preparation is better equipped in pharmacies, and hospitals are more equipped with infusion drugs than pharmacies. Conclusion: There are a great difference between 20 kinds of rare disease drugs, and provinces with better economic conditions, strong payment ability of medical insurance fund, abundant medical resources, and implementation of “dual-channel” policy are relatively better equipped with orphan drugs.