Sustainable agricultural ecosystem are the basic guarantee and condition for the sustainable development of society and economy. The identification of limiting factors is a crucial step to assess the sustainability, to work out the strategies and to implement comprehensive measures for sustainable development of agricultural ecosystem. As a case study, the limiting factors and regulation strategies for the sustainable agricultural ecosystem in Jiangpu county, Nanjing city are analyzed. The results show that the main limiting factors are the decreasing trend of arable land, frequent occurrence of ecological disasters and the weak ability against external perturbation of agricultural ecosystem. The countermeasures for promoting the sustainable development of agricultural ecosystem in Jiangpu county, Nanjing city, including the protection of arable land, the enhancement of the ability against external perturbation, and the control of ecological disasters are suggested.