The new rural cooperative medical system has achieved periodical achievements since its establishment. Nevertheless, there are many factors hampering the development of the new system, such as the high cost, the difficulties in fund procurement, the lack of management, the narrow coverage of benefit, the ineffective constraint to the designated medical institutions, the high fund balance rate, and the poor medical facilities and services in rural areas. Countermeasures are put forward to solve these problems, including improving the system design, expanding the coverage of the system, expanding the fund sources, reducing the financing costs, strengthening the fund supervision, enhancing the supervision of designated medical institutions, and improving the capacity of health services in rural areas.