Abstract: We have faced several challenges currently on the world. Global population, food, energy and environmental crises as cause-effects have made cycling ever more dangerous. With this background, agricultural problems have become more incomprehensible. From agro-ecological point of view, this paper emphasized identification of current weakness in ecological theory and proposed relative future preferential actions. Main theatrical weaknesses related to eco-agriculture had been identified as follows: 1) Synthesis of studies on environmental factors. There was the need to integrate research in such areas as soil, water, nutrition, climate, pollution, etc. for full understanding of field observations. Such examples were the decline in soil organic carbon in black soils in Northeast China and the reverse in South, the driving factors of soil acidification in main crop farmlands and the influence of soil texture on the accumulation and concentration of soil nutrients. 2) Agricultural biodiversity consisted of plant and animal genetic resources, natural enemy organisms, pollination insects and soil biota. However, current knowledge had mainly focused on the genetic resources of crops and animals with gross lack of systematic assessments on soil biodiversity, natural enemy resources and pollinating insect diversity. 3) Agricultural food webs were logically reduced to a four levels among the above five biodiversity categories with plants as the core. Plant interacted with soil biodiversity at farmland level, with natural enemy organisms and pollination insects at landscape level, and with husbandry at region level, respectively. However, little had been rarely known that these interaction patters and process. 4) With regard to the influence of intensive agriculture on ecosystem structure and function, the underlying relationship between intensive agriculture and ecosystem structure had neither been confirmed nor had the influencing of ecosystem structure processes on the related functions been clarified. In order to orient future efforts, a simplified "route-map" was proposed. In complex agriculture environments, soil quality investigation had taken priority, based on which land use (including farmland reconstruction and pasture establishment) was programmed. In complex agriculture organism communities, cultivation pattern regulation was advantageous. From this point, it was prudent to regulate husbandry, forestry and fruit plantations in sequence. At the end, cultivation and husbandry matched each other. In macrocosms of organisms and the environment, ecological risk assessment served as a start point. This was followed by pollution and technical hazard control, which eventually led to ecological restoration. For near future actions, it was suggested to lay priority on three urgent tasks. The first was to conduct soil quality census, except soil physical and chemistry property, biological characteristics needed detailed investigation. The second was to assess ecological risks based on soil quality, which involved soil inorganic phosphorus accumulation, soil organic carbon sink, CO2 emission from soils into the atmosphere, changes in food webs in soil ecosystems, etc. The third was to regulate agricultural cultivation patterns where first productivity would match second productivity. From an extended view, it was suggested to stress the study of economics and sociology of agriculture. Such areas as pricing mechanisms of agricultural products, investment scales and fundamental constructions of farmlands, economic costs of hazard controls and ecological restorations, and changes in rural social structures, farmer livelihood and welfare needed detailed studies. In conclusion, there was the need for a holistic vision and methodology of studies aimed at resolving current problems in agriculture.