There are many interests conflicts in green development, which need effective system arrangement to coordinate the interests of each party. Based on management practice of the Thames River basin, the Danube River basin, the Murray-Darling River basin and the Mississippi River basin, in order to realize green development, the comprehensive management is needed under the overall united management agencies so that interests integration is used to effectively solve the structural conflicts between economic construction and green development and effective institutional system is used to solve the interests conflicts of each party. On the basis of international benchmarking of green development experience, the Huaihe River basin should establish top level management agencies to overall conduct green development of the basin, scientifically allocate water resources and pollution discharge right, optimize industrial layout, set up and complete cost-sharing mechanism, transfer payment mechanism and examination evaluation mechanism so as to realize high-quality development through comprehensive management and comprehensive coordination.