Abstract: The stable operation mechanism is the foundation of new rural cooperative medical care system sustainable development. With the restriction of operation bottleneck result from the Stakeholder gambling among farmer, government and medical institution, the cooperative medical operation mechanism innovation needs to perfect financing mechanism, compensation mechanism and supervisory managerial mechanism; in particular, the government must design Institutional, perfect market supervising and managing reasonably, consequently meets farmer's basic medical health service need to the extent, ensure new rural cooperative medical care system sustainable development.