Abstract: Comprehensive clinical drug evaluation is an important technical tool for decision-making on drug supply. Traditional evaluation on health technology provides methodological references for comprehensive clinical evalu-ation of drugs. However, data from clinical trials for orphan drugs are often insufficient. It is difficult to evaluate the clinical and economic value of orphan drugs by using the criteria of ordinary drugs. Particularity of orphan drugs makes it difficult to use the traditional evaluation methods for health technology. Multiple criteria decision analysis explores the comprehensive value of drugs from different angles. It promotes the transparency and scientific thinking on the basis of evidence-based medicine, improves the quality of decision-making, and thus provides a possible 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 trial stage, and no methodological guidelines is available. In order to optimize 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 China Alliance for Rare Disease organized experts in related fields to formulate this consensus, aiming to provide standardized methodological guideline to the comprehensive clinical evaluation of orphan drugs.