Abstract: Modern agronomy (initiated by experimental sciences of reductionism thinking and motivated by industrialized European revolution) had led to astronomical increase in agricultural production, but at a huge cost of destroying the natural base of agricultural sustainability. The prevalence of reductionism thinking disassembled agronomy into smaller disciplines in university education system across the globe. This led to the so-called “Therapeutic Intervention” in applied fields of agriculture, which in turn posed current problems in modern agricultural systems. Such problems included soil degradation, loss of agro-biodiversity and food safety due mainly to over-use of synthetic fertilizers and pesticides. Using crop cultivation/farming systems and plant genetics/breeding, the second-grade disciplines of agronomy as examples, the focus of the former was under community scale and that of the latter was under population scale, in terms of ecology. Comparative review showed that most of the problems of modern agriculture occurred beyond ecosystem scale. It was therefore imperative to gradually reframe agronomy and its educational systems with the goal of developing sustainable agricultural production strategies. In this paper, the author proposed bridging agronomy with ecology. This posed agroecology as a core discipline, upon which crop cultivation, cropping system and crop genetics/breeding research was regulated and broadened. These sub-disciplines of agronomy used agro-ecosystem management as a core applied system that integrates modern biological, ecological, information and material engineering. Methodologically, it paved a practical path to sustainable modern agriculture by integrating China's archaic deductivism thinking with western neoteric reductionism thinking.