Abstract: Traditional reform of environmental protection department, which depended heavily on both the expansion on powers and increase in dependency, can not avoid problems of excessive amount of sections, structure-complexity, and coordinative barriers.Adhering to the idea of ecosystem management, we should focus on the function intergration and sector restructure, so as to refine the basis of environmental management.The ideal design of super-environmental-ministry system should contain two parts.The first is theoretical logic, which includes organization structure, ecosystem management and externalities.The second is empirical logic, which contains successful experience at home and abroad.The balance of political power and interests is the sole criterion of the approaches.Generally speaking, central-level reform depend more on the political and experimental logic, while local-level reform may adopt both the experimental and theoretical logic.Gradual reform should leave more space for local experiments, and that will help to realize the unity of triple logic on the reform of SEM system.