The calculation of ecological compensation standard is the key to establishing ecological compensation mechanism. In the process of establishing the model, we follow the metastatic pattern of water resources' ecological economic value. The model considered the discharge of pollutant between administrative area, pollutant absorbing capacity of river basin, ability of pollutant treatment and other factors, so as to closely combine ecological compensation standard with the total pollutants and water resource value (WRV). On this basis, total pollutant control model (TPC) and WRV model were constructed, the former model complied with properties of regional socio-economic, environmental resources and water environmental carrying capacity while the latter reflected the situation of resources, environment and socio-economic. And further, the ecological compensation standard coupling model of TPC-WRV was constructed by these two models, and the dilution water was introduced as a coupling pathway. Applying this coupling model to Xiao Honghe of China, the ecological compensation standard of four counties from 2008 to 2012 was calculated. The results show that the compensation value of Xiao Honghe basically presented increasing trend from upstream to downstream during 2008 to 2012. This study develops new ideas to comprehensively quantify the ecological compensation standard of river basin.