The traditional agronomy was initiated at the tide of experimental science in modern agricultural academia. Because of the apparent achievements of Industrial Revolution, the comprehensive grasp of agro-ecosystem in understanding and developing agronomic science has subsequently not been recognized. As a consequence, humanity has to confront the double crises of food security resulting from the degradation of agro-ecosystems and productivity decline, and the food safety resulting from the deterioration of agro-environment and food contamination. Traditional agronomy has positioned bio-organizational levels under ecosystem scale both as a discipline and as a specialty in China. This has been the root of production and environmental problems in modern agricultural practices. In this paper, we proposed reframing traditional agronomy by putting agroecology at the core of the theoretical aspects and agro-ecosystem management at the core of applied subjects. The basic framework and technological choices of agro-ecosystem management are addressed in detail. Also the connotation, extension and development perspectives of agro-ecosystem management are discussed in detail.