The water pollutant loads of the upstream regions should be strictly controlled in order to protect the water quality of the water source in the downstream areas. In this way, the economic and social development in upstream regions will be adversely influenced. So the ecological compensation mechanism should be established to compensate the protection behavior of the upstream regions. The water quality and water quantity are synthetically considered in this paper to develop the ecological compensation standard model of water resources protection. Firstly, the environmental hydraulics method is employed to describe the influence relationship of the water environment between the upstream and downstream regions. Then the water quantity factor is also considered to reflect the scope and degree of the water environment protection in the upstream region. On the other hand, the direct and indirect costs of the water environment protection are calculated with the method of environmental economics. At last, the environmental and economic methods are combined to establish the compensation standard model of water resources protection. The model is applied to calculate and analyze the compensation standard of the Xinanjiang River basin as a case study. The model developed in this paper can flexibly and objectively describe the environmental and economic relationship of the ecological compensation, so it is helpful to provide support for the establishment of ecological compensation mechanism in China.