Based on the idea of eco-compensation, this paper explicates the necessity and theory basis of compensation mechanism of water pollution control, and discusses its discipline, object, mode and other correlative issues. According to actuality of the three gorges reservoir and its upstream areas, advices on the construction of compensation mechanism of water pollution control by government were brought forward.The construction and improvement of compensation mechanism of water pollution control can relieve the fund shortage of water quality protection in three gorges reservoir and its upstream areas, and stir the enthusiasm of local governments of upstream and downstream areas to control water pollution, which have realism significance to water quality protection and water pollution control of the whole drainage areas.