The invention discloses a clinical acupuncture evidence-based decision support system and an application method thereof. The system comprises a data preprocessing module, a data importing and updating module, an electronic medical record module, a diagnosis decision-making module, a treat decision-making module, a system auxiliary module, a result output module and a databank. According to the system, decision-making mechanisms of the evidence-based medicine are blended into a decision-making scheme of a CDSS (Clinical Decision Support System), the evidence utilization is used as the core, an electronic medical record technique is embedded into a clinical acupuncture diagnosis and treat process so as to integrate an evidence-based databank and a data mining model, a clinical acupuncture evidence-based auxiliary support system in which the evaluation, storage, analysis and utilization of acupuncture research evidences are integrated is established, and a convenient and rapid man-machine interaction platform is provided for the effective utilization of the acupuncture research evidences. With the adoption of the system, the requirements of doctors in the overall clinical diagnosis and treat process are met well, and the alternative thinking process of diagnosis and treat is effectively supported, so that a treat scheme which is proposed finally is an optimal scheme obtained from literature evaluation, so that the clinical acupuncture evidence-based decision support system has relatively high clinical adaptation.