Based on the stakeholder theory and a case study in Baoji area, this paper establishes the evaluation index system of the new rural cooperative medical system（NRCMS） to evaluate the capability of medical care security for farmers. This paper uses Entropy method and the Analytic Hierarchy Process to determine the weight of each index as well as Fuzzy evaluation method to conduct a comprehensive evaluation on security capabilities of new rural cooperative medical system in Baoji area. The result shows that the security capability of government and cooperative medical service agencies is stronger while the security capability of designated medical institutions is general. Therefore, this paper puts forward some major suggestions on how to improve the security capability of new rural cooperative medical service in Baoji area: to increase investment in construction of medical infrastructure, to allocate more medical care workers with professional qualifications and to strengthen the supervision of pharmaceutical drugs.