Abstract: Low N use efficiency with high environmental impact is a worldwide problem which may be resolved by reduce target yield and N input in developed countries with surplus arable land and small population. In China, whose population is the largest and areas of arable land per capital is very limited, different approach should be made in order to reduce the environmental impact while the crop yield and productivity can be maintained or even increased at the same time. Therefore, the N input should be optimized to reach the harmonious point between high yield and sound environment. A key project on fate and efficient use of nitrogen fertilizer in two main agroecosystems was approached by NSFC recently, which will be carried out by a group of multidisciplinary scientists from soil science, plant nutrition, plant breeding and genetics. The fate of chemical fertilizer N in wheat-maize rotation in north china plain and rice-wheat rotation in Taihu area should be quantified at different rates of N application in field studies with the aim of modeling. The recommendation for the optimum rate of N application will be evaluated from the harmonization of high yield with the environment protection. And by using GIS technique, the principle for the recommendation of the optimum rate of N application at both field and regional scales will be studied and developed in accordance with the situation of Chinese countryside. The N-efficient genotypes of rice, wheat and maize will be screened out, and the physiological and genetic mechanisms with emphasis on root biology will be studied.