Equity and efficiency, as two essential parts of social security, always influence construction of China’s new rural cooperative medical care system. The new rural cooperative medical care system is a rural social security system particularly intended to make it more affordable for the rural poor. It is a multi-channel fundraising system with fund of comprehensive arrangement for serious disease composed by the government, collectives and individuals. Since its implementation, it has made considerable achievements, but there are still many apparent and hidden problems. Through analyzing existing problems in the implementation of new rural cooperative medical care system, from the perspective of equity and efficiency, it reached the conclusion that government should take corresponding responsibilities. At the same time of constantly increasing efficiency, it is recommended to attach importance to the equity, so as to realize the objective of improving the security level of new rural cooperative medical care system.