In order to evaluate the emergy output structure and its trend of agro-ecological economic system of Jiangxi Province, and provide the basis for the formulation of the countermeasures for the sustainable development of Jiangxi agricultural system, based on the studying input emergy and output emergy of agro-ecological economic system of Jiangxi, the author constructed the structure of various emergy index and analyzed the structure, function, efficiency and development trend of agro-ecological system in Jiangxi Province. The results showed that the rate of emergy input was higher organic emergy much more, industrial auxiliary emergy was little, system in self sustaining production status with strong tradition and higher conservative; The rate of net emergy output was low, the system was in the stage of labor-intensive, low intensive degree, and low production efficiency extensive; the environmental loading ratio was in larger growth, which indicated that the system rose ceaselessly on emergy using technology and the environmental pressure were getting bigger and bigger; sustainable development index of system emergy was 0.176-0.225 which was far less than 1, the system was a typical consumption-based ecological system, output emergy obtains by consuming more resources. Agricultural system of Jiangxi should optimize the emergy input and output structure, improve energy efficiency and production efficiency, increase the devotion of technology ingredients, pay attention to the coordination and unity and system of ecological management of rationality, combining the modern high-tech with the essence of traditional agricultural technology, change the traditional extensive mode to modern scientific technology, highly intensive and high efficiency.