Inclusive supplementary medical insurance (hereinafter referred to as “inclusive insurance”) has gradually become an important force in the multi-level healthcare security for rare diseases. This article constructs an indicator evaluation system to assess the public-private partnership models and rare disease security index of 32 representative inclusive insurance products, and explores the impact of public-private partnership models on inclusive insurance participating in rare disease security through comparative analysis. Research has found that the level of rare disease security for most inclusive insurance products led by government is relatively high, while the level of rare disease security for most inclusive insurance products promoted by government is relatively low. The average and maximum values of the rare disease security index for government-led products are higher than those for government-promoted products. Based on the analysis above, this article proposes policy recommendations for optimizing the security of rare diseases in inclusive insurance: strengthening the collaborative governance between the government and the market, promoting the participation of inclusive insurance in health management, strengthening the supervision of inclusive insurance products, and promoting data sharing and technological empowerment.