The calculation of an ecological compensation standard is an important, but also difficult aspect of current ecological compensation research. In this paper, the factors affecting the ecological-economic system in the Xiao Honghe River Basin, China, including the flow of energy, materials, and money, were calculated using the emergy analysis method. A consideration of the relationships between the ecological-economic value of water resources and ecological compensation allowed the ecological-economic value to be calculated. On this basis, the amount of water needed for dilution was used to develop a calculation model for the ecological compensation standard of the basin. Using the Xiao Honghe River Basin as an example, the value of water resources and the ecological compensation standard were calculated using this model according to the emission levels of the main pollutant in the basin, chemical oxygen demand. The compensation standards calculated for the research areas in Xipin, Shangcai, Pingyu, and Xincai were 34.91 yuan/m3, 32.97 yuan/m3, 35.99 yuan/m3, and 34.70 yuan/m3, respectively, and such research output would help to generate and support new approaches to the long-term ecological protection of the basin and improvement of the ecological compensation system.