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 be confronted 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 fossil agricultural practices. In this paper, we proposed reframing traditional agronomy by putting agro-ecology to core of theoretical system and agro-ecosystem management to core applied subject. The basic framework and technological choices of agro-ecosystem management were addressed in detail. Also the connotation, extension and development perspectives of agro-ecosystem management were discussed in detail.