From the angle of ecological compensation funds management in Huaihe River Basin, the importance of establishing a mechanism for Huaihe River Basin ecological compensation funds management and typical problems faced are analyzed. Relevant countermeasures such as establishing institute of Huaihe River Basin ecological compensation fund management, broadening the channel of ecological compensation fund and the application range of the ecological compensation fund, searching multiple ways of compensation, improving the legal system and supervisory mechanism are proposed. The purpose of this paper is to provide reference to improving the ecological compensation mechanism of Huaihe River Basin, improving the utilization level of compensation funds, planning and coordinating the regional ecological compensation.