The subject and object of ecological compensation in the Dongjiang River Basin were divided based on the water resources allocation scheme. The value of water resources and ecosystem service in the region, the expense of protection and improvement and the ecological compensation fees and standards, based on the value of water resources, were calculated. The Dongjiang River Basin ecological compensation mechanism and system were discussed. It is recommended to adapt downstream compensating upstream mode, based on the water resources value, combined with national policies. In terms of cash management and operation, the Dongjiang River Basin ecological compensation fund committee is recommended to establish, which is responsible for fund management, project establishment, evaluation and audit and supervision and inspection of implementation process.