The new rural cooperative medical system (NCMS) has achieved remarkable results on the whole. However, in the actual operation process of the new rural cooperative fund, there are still outstanding problems such as low evaluation of the NCMS, low efficiency of medical treatment, complicated reimbursement process, and ″passive participation of farmers″, which affect the satisfaction of participating farmers in the new rural cooperative fund.. Based on the perspective of participating farmers and the operation data of the 2015 new rural cooperative fund in L city, this article uses the structural equation model to systematically analyze the main factors affecting the satisfaction of participating farmers and sorts out possible solutions to improve and optimize the NCMS on the basis of data analysis and practical feedback. The result indicates:(1) The management level and medical treatment process have more significant impact on the farmers’ satisfaction, and the least significant variable is the system design. (2) The medical level and medical expenses in the medical treatment process have the most direct impact on the farmers’ satisfaction, and the influence of the medical service attitudes of the designated medical institutions is weak. It indicates that farmers’ satisfaction with the performance of the new rural cooperative fund is strongly related to the micro-factors such as the treatment process of their own diseases, the burden of treatment costs and the final treatment effect. (3) In terms of management levels, the medical service reimbursement procedures and policy propaganda have a significant impact on the farmers’ satisfaction, while the transparency of medical service charges and the service attitudes of the new rural cooperative fund managers have the less impact, which reveals that the farmers are more concerned about the basic policies, core systems, and expense reimbursement of the new rural cooperative fund directly affecting their interests. (4) The influence of system design on the farmers’ satisfaction is not very significant. It is potentially due to the cognitive ability of farmers, which limits their understanding of the complex NCMS and its derivative system. It objectively causes farmers ″information asymmetry″ in the perception of the NCMS and their judgment on the importance of the system. This paper puts forward the policy recommendations for optimizing the performance of the new rural cooperative fund and further improving farmers’ satisfaction as follows: (1) in response to the shortcomings and problems of the service supply mechanism, the government should construct high-quality medical service supply mechanisms under the guidance of the principle of ″openness, competition and cooperation″; (2) The government needs to strengthen the cultivation of farmers’ active participation awareness and the construction of participation mechanisms by strengthening policy propaganda and expanding effective institutionalized participation channels; (3)The government should reform the traditional management of the new rural cooperative fund in, integrate internal and external management resources, and continuously promote the capacity building of the government management institutions of NCMS; (4) The government should introduce the performance evaluation tool of new rural cooperative fund, and through continuous evaluation, the evaluation results should be ″linked″ to the input of financial resources to give play to the ″leverage″ and ″guidance″ functions of the performance evaluation of the new rural cooperative fund.