Abstract: Comprehensive drug evaluation is an important technical tool for decision-making on drug supply. Traditional health technology of evaluation provides methodological references for comprehensive clinical evalu-ation of drugs. However, there is a lack of sufficient data from clinical trials for orphan drugs. It is difficult to evaluate the clinical and economic value of orphan drugs with the criteria of ordinary drugs. Particularity of orphan drugs makes it difficult to use the evaluation methods of traditional health technology. Multi-criteria decision analysis explores the comprehensive value of drugs from various aspects. It promotes the transparency and scientific thinking of evidence-based decision-making, and improves the quality of decision-making, and thus provides a potential solution to the comprehensive clinical evaluation of orphan drugs. However, its application in the comprehensive evaluation of orphan drugs in China is still in its infancy and exploratory stage, and there is a lack of methodological guidelines. In order to improve the construction of a diversified system for comprehensive clinical evaluation of orphan drugs in China, the Multi-disciplinary Team for Rare Diseases of Peking Union Medical College Hospital and the National Rare Diseases Committee organized experts in related fields to formulate this consensus, aiming to provide methodological standards for comprehensive clinical evaluation of orphan drugs.