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Eco-compensation is an important mechanism when applying the theory of ecosystem services to practical development, which translates the external and non-market value of the environment into real financial incentives for local actors. Scientifically formulating feasible and credible compensation standards is the most critical and key step to adjusting the benefits received by environment protectors and beneficiaries. The Inner Mongolia agro-pastoral zone is an important ecological area with an undeveloped economy in Northern China. The implementation of eco-compensation policies contributes to ecological restoration and poverty alleviation. Taking Horqin Left Back Banner, Inner Mongolia, China as a study case, a quantitative model of a non-point source pollution eco-compensation program was established by using emergy synthesis—a thermodynamics-based method in ecological economic systems—to create a comprehensive eco-compensation standard. The results showed that the eco-compensation amounts for non-point source pollution were generally below 10% of the regional gross domestic product (GDP). A 11–20% reduction in fertilizer would be accepted according to the field investigation and the optimal eco-compensation strategy reduced the phosphate fertilizer application by 20% with a compensation standard of $379.63/ha/year, which was similar to the farmers’ willingness to accept compensation. For the accurate creation of a non-point source pollution eco-compensation program, the emergy synthesis overcomes the inconsistency in the quantification of the material flow, ecological flow, and economic flow, guaranteeing the sustainable implementation of non-point source pollution eco-compensation projects.

Determination of the Agricultural Eco-Compensation Standards in Ecological Fragile Poverty Areas Based on Emergy Synthesis