Objective: To identify the key problems of the health care system implementation and to analysis the problems, and provide decision making for policy administrators. Methods: Literature research, field survey and expert panel method of questionnaire survey were used in the study, TOPSIS comprehensive evaluation method was used for multidimensional comprehensive evaluation of the key problems in health care system implementation. Results: Ranking problems were fund raising, fund implementation and management, the ability of economic protection, supervision and the utilization of health service equity and management system. Conclusions: The results show that lack the reasonable financing mechanism, stable fund source and the regional difference of the system, contradictions in the implementation of the fund’’s balance of payments and the various types of account management policies, the incidence of catastrophic health expenditure are still prominent problems in the implementation of the health care system. So promoting the medical insurance system of urban and rural residents financing mechanisms, from fixed financing to transition in disposable income as the base of financing, controlling the unreasonable growth of medical expenses to ensure the fund’’s balance of payments, improving the overall level of health insurance and the effective promotion of serious illness insurance policy are the fundamental solutions to the problem of the health care system.