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.