Under Super-Ministry system, the number of government agencies is reduced while the responsibilities of a single agency are increasing, and administrative efficiency is improved, however, the concentration of power and sector interests makes interests groups much more stubborn than ever. In order to prevent the shortcomings of sector interests of government departments, the intergovernmental coordination should be consolidated. Horizontally the coordination of governments at the same level should be encouraged by power restriction and interests balance, longitudinally the effective restriction mechanism should be implemented while the initiative of the government at the lower level should be increased. Agency reform should stick to power decentralization direction, emphatically consider the factor of department interests, design and implement the effective monitoring and restricting mechanism, set up and perfect the division of labor and cooperation between decisionmaking agencies, consultation agencies, executive agencies, monitoring agencies and information agencies. In addition to building coordination institutions and strengthening the central government regulation and management on local governments, the power of intermediary organizations and social organizations should be cultivated.