Watershed ecological compensation is an effective economic policy measure for water ecology conservation and water environment management. This study constructed an eco-compensation mechanism under the double control of water quality and quantity, which consisted of the water quality control module, the water quantity control module, and the double control compensation value module. The pollution loss water quantity and the river habitat compensation water quantity were calculated, and the water quality achievement or excess and water quantity surplus or deficit were identified to divide the multi-scenario compensation mode and obtain the double control compensation value. The Bai River Basin in Nanyang, China, was selected as the case study, and the double control compensation value of the three counties in the basin was calculated from 2015 to 2018. The results showed that the water quantity compensation value of all counties was higher than the water quality compensation value, indicating that the water quantity has a greater impact on the water environment compared with water quality, and the ecological water demand of rivers needs to be guaranteed while strengthening water pollution treatment. The compensation mode all belonged to the double control mode. The double-control compensation mechanism had a distinct advantage over the single-control compensation, indicating that water quality and quantity should be considered in the compensation programs to maintain healthy ecological conditions in the water supply. The research results provide ideas for the quantification of eco-compensation and the formulation of long-term ecological protection mechanisms.