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Ecological agriculture (eco-agriculture) is an approach to agriculture that seeks a balance between ecological and economic benefits to promote the sustainable development of both. This paper proposes a scientific method for analyzing the environmental and economic effects of eco-agriculture and simulating their long-term trend. Here, we focus on the eco-agriculture system of Kongtong District, Pingliang City, Gansu Province, China, and we build a system dynamics model named “AEP-SD” to evaluate the integrated effects of the system from 2009 to 2050. Under business as usual conditions, simulation results show rapid improvement until a peak is reached in 2027, after which the system will decline gradually. The model identifies some defects and disadvantages of the current agriculture system, such as the excessive increase of cattle slaughter, unstable production of methane, slow development of organic agriculture, and unsustainable energy structure. System improvement policies are offered and then proven by the model that they can indeed reduce the negative effects and eliminate the potential risks of system decline. [Copyright &y& Elsevier]