Abstract: The authors reviewed the developmental history and characteristics of agroecology, and pointed out that the research areas of agroecology were broadening in both macroscopic and microscopic aspects, and the researches were going more deeply. On the macroscopic level, the investigation of agroecology was expanding from a pure macroscopic study of agricultural biology to a sociological study concerning the issues related to agriculture, farmer and rural areas. The research works shifted from the relationships between structure and function of agroecosystem to the food system. The major task was to study the impacts of the energy and material flow in agroecosystem on the social and economic development, and the regulation of food system by policy and laws from the eco-economic perspective. Modern agroecology emphasized the awakening of social ecological consciousness and the important role of ecological consciousness which played great roles in the protection of argoecosystem and the promotion of pollution-free production. Therefore, in western countries, community movements or actions were important ways that agroecologists relied on to make government, production units, sell units and administrations accept the agroecological concepts, act in compliance with agroecological laws and ensure the health and efficiency of the food system. These activities had become essential subjects in the education, research and practice of modern agroecology, which involved all processes in agroecology, including scientific research, demonstration and its extension of experiments, promotion by society or association actions, spontaneous participation of publics. All these efforts embodied the feature of the modern agroecology. On the microscopic level, modern agroecology was entering the age of molecular agroecology. Molecular agroecology employed the state-of-art techniques of modern biology and introduced the theories and assays from systems biology to unveil the underlying relationships and mechanisms of the structure and function of agroecosystem. With the development of modern biology techniques, especially the breakthroughs of environmental (meta-) genomics and proteomics, molecular agroecology largely enriched our knowledge of the unknown biological world. The ability to analyze biodiversity and genetic diversity in depth enabled molecular agroecology to examine the processes and mechanisms underlying ecosystem development on the molecular level, which fueled the transformation of agroecology from a qualitative and half-quantitative study into a quantitative and mechanism study. This change urged the agroecologists to keep pace with the times. The agroecologists needed to improve their knowledge structure and scientific research ability in order to follow the transformation of agroecology from traditional science into modern science. This article took many case-studies as examples to demonstrate the necessity and importance of this scientific development, and aimed at inspiring introspection and thinking among peers.