Abstract: In order to explore food security, high resources use efficiency and environmental friendly pathway for the coordinated and green developed agriculture in the food production and food consumption system, we constructed the "soil-crop-livestock-family-environment" ("food chain system" in short) research system. Using the material flow and metabolism theories, a nutrient flow model had been developed, and was used to evaluate the nutrient flow and control mechanisms of food chain system. After more than ten years systematic studies, the research team obtained the following main results:(1) Develop the pyramid framework for nutrient flow of the food chain, and the food chain nutrient flow model. By analyzing nutrients behavior in the "Soil-Crop-Livestock-Household-Environment" system, we found that the nutrient flow from "Soil-Crop-Livestock" to "Household" sector was in the shape of pyramid. The shape of pyramid determined the productivity, nutrient efficiency and environmental effects of the food chain system. The "Household" consumption at the top of pyramid was the driving force of nutrient flow in the whole food system, meanwhile, determined the nutrient efficiency of whole system. "Soil-Crop-Livestock" was located at the bottom of pyramid, supporting the "Household" consumption sector at the top. It determined the total nutrients flux and acted as the core of nutrients management. Based on this, the NUFER (NUtrient flows in Food chains, Environment and Resources use) was developed, the parameter set was build and quantification of nitrogen (N) and phosphorus (P) flows, use efficiencies and environmental emissions at the national and regional scales had been done. (2) Spatial and temporal analysis of N and P flows, use efficiencies and environmental costs in the food chain system. We quantified the spatial and temporal characteristics of N and P flows, efficiencies and environmental emissions in crop and animal production sector, and the whole food chain in China. We identified the contribution of nutrient losses form soil-crop system, livestock and human consumption. We also developed the concept of food N (P) cost and found that the resource and environmental costs of food production and consumption in China had increased rapidly, far exceeding the developed countries. (3) Identifying the driving forces of nutrient flow in the food chain and the options to improve nutrient efficiency and reduce environmental losses. The key sector that determined nutrient efficiency had been identified. Urbanization, diet changes and development of livestock production were the main driving forces of the accelerated nutrient flow in food chain system. We also explained the effects and mechanisms of increasing imports of food and feed, optimizing dietary and improving the nutrient management in agriculture production on improving food chain systems. We also found that the coupling of crop and livestock production, improving utilization of livestock manure was the key to reducing chemical fertilizer use and environmental losses, and was also the key for achieving green development of agriculture and sustainable food systems.