Objective To sort out the policies related to rare diseases in China, analyze and summarize the focus and potential problems of relevant policy texts, and provide decision-making references for the subsequent formulation and improvement of policies in the field of rare diseases in China. Methods We searched for relevant policy documents in the field of rare diseases at the national level from 2018 to 2023, constructed a three-dimensional analysis framework based on content analysis of “policy tool-stakeholder-policy strength” in the field of rare diseases in China, and conducted cross-analysis between policy tools, stakeholders, and policy strength. Results Finally, 39 policy texts were included. There were 112 policy tool dimension codes, with environment-based, supply-based, and demand-based tools accounting for 62.5%, 30.36%, and 7.14%, respectively. There were 229 stakeholder dimension codes, including 42.79% for government departments, 19.65% for medical institutions, 19.65% for corporate units, and 17.90% for patients and their families. The average score for policy strength was 2.2 points. Cross-analysis showed that government departments had the highest proportion in the dimensions of supply-based, environment-based and demand-based tools (45.76%, 43.45%, 32.00%, respectively). The policy strength of environmental tools was the strongest (124 points). The policy strength of government departments was the strongest (78 points). Conclusions There is a certain imbalance in the design and configuration of rare disease policy tools in China, and there is uneven distribution of rare disease policies among stakeholders. Although the overall effectiveness of policies in the field of rare diseases is showing a positive growth trend, there may be a mismatch between policy tools, stakeholders, and policy strength.