Abstract: Abstract: The aim of agro-ecological compensation is to eliminate the negative effects during agricultural production, and promote the strategy implementation of environment-friendly agriculture. At present, agro-ecological compensation standard is greatly affected by the temporal and spatial variation of value, and the inaccuracy of input cost calculation result. Emergy is an important advanced technology in calculation of material inputs and efficiency of agricultural ecological protection quality. The paper gave the study method of agro-ecological compensation standard based on the conversion between emergy and value, as well as the process to calculate agro-ecological protection cost and benefit. On the basis of defining the components within the system, and allowing the identification of inputs and output of agricultural production, the annual emergy flows were calculated. Then the emergy indicators were determined to evaluate the performance of the agriculture environmental system. Taking the upstream of Guanting Reservoir in Yongding River basin as study area, on the basis of calculating the emergy of renewable natural resources (R), non-renewable natural resources (N), materials (M) and services (S), the total emergy, renewable emergy and non-renewable emergy of Yongding River basin agro-ecological system were 3.80×1016, 1.59×1016 and 2.21×1016 Sej/hm2 respectively. According to the calculating data of ESI (Environmental Sustainability Index for the management of agricultural output and environmental load, assumed to obtain the largest production with the minimum of environmental damage), the sustainable development degree of basin agricultural production was determined. The index of ESI was calculated by transforming natural resources, agricultural products, and environment-friendly agricultural production economic input into emergy flow. Combining the calculation results of emergy, fundamental quantity ESI is 0.1056, which is far below 5. Therefore, unsustainable input or output accounts for a large proportion during basin agricultural production, which indicates that agro-ecological system of study area is not sustainable, and to adopt agro-ecological compensation measures is necessary. The respective emprice of the environmental benefits (R, N, M, S) supplied by the reserve was evaluated corresponding to the biomass production. By combining high productivity and good market prices, the emergy exchange ratio reveals that the payment for the environmental services is realized. Considering the environmental flows that the farmers take from protecting nature without payment, a value balance based on the beneficiary-pays rather than the producer-pays principle, agro-ecological compensation was calculated as commercial transactions where the environmental service is acquired from the watershed farmers. The option proposed in the paper indicates that by the adoption of the emergy accounting method, the government and producers would be responsible for a portion of the PES, and the emprice calculated for the environmental support and the environmental benefits of farmland should be used to decide who will bear the responsibility for making payments for environmental services. To realize the sustainable development of basin agriculture, the government and beneficiary sectors will compensate farmers soil loss preventive costs 400 million Yuan. The compensation standard calculation method of agro-ecological system in the light of emergy is feasible. Further studies are necessary on agricultural production environmental services, such as the maintenance of the biodiversity and natural biocenosis, and hydrological services.