This study is based on the realities of challenges within the field of rare disease treatment, as well as the concept of value-based healthcare. By analyzing treatment plans, rehabilitative care, cost-sharing, prospects for drug development markets and investment returns, as well as policy support, the paper delves into the complexities and diversities of rare disease treatment. Within the research, the focus is on the challenges of rare disease treatment, leveraging the principles of value-based healthcare. It discusses how personalized treatment plans, interdisciplinary collaboration, and reasonable cost-sharing can enhance patient treatment outcomes and quality of life. The article employs methods such as literature reviews and case analyses to deeply explore and analyze rare disease treatment from various angles. The research findings indicate that personalized treatment plans and interdisciplinary collaboration can significantly enhance treatment outcomes and quality of life for rare disease patients. Reasonable cost-sharing models and trends in drug development markets present opportunities for the sustainable growth of the rare disease field. Additionally, policy support and international cooperation mechanisms play vital roles in advancing rare disease treatment. Based on these research findings, the article proposes future research prospects, including strengthening data collection and analysis, deepening international collaboration, and optimizing drug development strategies.