Background Rare diseases are one of the major challenges in the era of precision medicine and reflect the social security level of minority groups. This study aimed to investigate healthcare service utilization and health security of patients with rare diseases in China. Methods From 29 provinces of Mainland China, 7,747 visits with eight common rare diseases who were linked to the national insurance database between 2014 and 2016 were selected as the study population, whose demographic and healthcare service information was collected from China's national monitoring system for health service utilization of patients with healthcare insurance. Univariate analysis was performed to describe the basic statement of healthcare service, such as visit type, institution type, length of stay, healthcare insurance utilization, and the results of disease burden for different groups and its factors were analyzed by multivariate analysis. Results Medical treatment from general tertiary hospitals was sought by 61.4% of the patients with rare diseases. Of the total treatment cost (TTC) of 40.18 million Chinese Yuan, 63.3% was paid by basic health insurance, and 54.2% of the medical cost resulted from medicine expenditure. Demography, geography and social-economic factors, security level, and health institution situation had an effect on the TTC. The correlations between these factors and TTC were different for outpatients and inpatients. Reimbursement rate had the highest effect on inpatients' TTC. Basic insurance was effective for providing support for patients with rare diseases that involved high costs; however, the coverage was limited. Conclusions Healthcare insurance is an effective safeguard for patients with rare diseases; however, affordable and accessible treatment is still lacking for such patients. There remains a need to further improve the diagnostic and treatment technology for rare diseases and expertise among doctors, as well as the security level of healthcare policies.