Abstract: Cybernetic theory, information theory and system's theory play an unique role on the formation of the disciplinary structure of agroecology during the early stage of agroecology development in China. In the discipline of agroecology in China, attentions were not only paid on energy and material flows, such as the structure of species, population, community, ecosystem and landscape, but also on information flow including natural information flow and artificial information flow, and on capital flow, including the value chain and its monetary representation, that is capital flow. Agroecology in China paid attention not only on the energy and material transformation structure of agroecosystem such as producer, consumer and decomposer, but also on the control and regulation of agroecosystem structure including natural control and regulation structure, and artificial control and regulation structure. In artificial control and regulation structure, direct control and indirect control approaches could be identified. Crop cultivation and animal raising actions exerted by the farmers on farm belong to direct control approach, and the market situation, government policy, national legislation, social tradition, education and information transmission which could affect the action of the farmers on farm, belong to indirect control mechanism. This disciplinary structure of agroecology based on cybernetic theory, information theory and system's theory is essential to further exploration of the excellent traditional Chinese agricultural practices, to stimulate the thought on basic and applied agroecology research, and to open up new approach for the ecological transformation of agriculture in this information era.