公平与效率作为社会保障的两个方面，始终影响着中国新型农村合作医疗制度的建改。新型农村合作医疗制度作为一项以政府扶持、农民互助共济的“大病统筹基金”的农村社会保障制度，在实施以来，虽取得了一定的成效，但仍然存在诸多隐性与显性问题。笔者通过分析新型农村合作医疗制度在实施过程中出现的问题，从公平与效率的角度，指出政府应该承担相应的责任，在效率不断提高的当下，应着重实现公平，从而达到提高新型农村合作医疗制度的保障水平的目标。

Fairness and efficiency, which are the two aspects of the social security issues, have been affecting the construction and reform of the new rural cooperative medical system in China. As a new type of rural social security system with fund of comprehensive arrangement for serious disease which gains government support and farmers help each other, since new rural social security system implemented , although it has made some achievements, there are still recessive and dominant many issues. In this article, through the analyzing problems of the new rural cooperative medical care system in the implementation process , the government are pointed out that they should undertake corresponding responsibility from the perspective of fairness and efficiency. The efficiency improving increasingly at the moment, we should emphasize fairness so as to improve the security level of the new rural cooperative medical care system.