Abstract: Based on the theory of conservation of substance "input = output + surplus" in substance flow analysis(SFA) method, N nutrient balance model of agro-ecosystem in China was built. Data obtained from China agriculture statistical report in 2004 and parameters acquired from recent references, input, output and surplus of N nutrient in agro-ecosystem of China were estimated for appraising environmental effect, results were shown as follows: N loss through emission, denitrification, plant transpiration, leaching and corrosion was 1132.8×10⁴ t in 2004, N surplus was 1301.2×10⁴ t in agro-ecosystem, and high environmental risk arose by these two parts of N nutrient existing in southeast of China and some central regions. For sake of decreasing high environment risk, some measures were put forward in this paper that chemical N fertilizer application rate must be optimized, and organic N fertilizer and chemical N fertilizer must be cooperated, it was also necessary to work out the rational pattern of planting and extending precision fertilization.