The paper aims at providing a framework to calculate the agro-eco-compensation standard based on the systems agro-ecological concept of embodied energy as emergy. We have proposed a calculation system of eco-compensation standard for sustainable agricultural development based on the convertibility between emergy and price. According to our calculation, the total energy of agricultural production in Yongding River Basin was 3.45 E + 16 Sej/ha (the unit emergy value, expressed in solar emergy joules per unit) in terms of the renewable resources, nonrenewable resources, material inputs, and service costs. The energy of renewable and nonrenewable resources was 1.59 E + 16 and 1.86E + 16 Sej/ha, respectively. The ESI (environmental sustainability index) of the study area was 0.1056, indicating that its agricultural production was in a seriously unsustainable condition. To realize the sustainable agricultural production in the watershed, the downstream governments should pay $21.81 M (¥135 million) approximately to upstream governments for water and soil conservation. The results of the present study suggested that the emergy-based calculation method of agro-eco-compensation standard is feasible to a certain degree.