In order to estimate the nitrogen balance in cropland of China, identify the fate of nitrogen and the possibility of nitrogen pollution, and finally put forward strategies to keep rational nitrogen application in the cropland and to limit the environment problems arising from the overuse of N fertilizers. A computer simulation model of carbon and nitrogen biogeochemistry in agro-ecosystems (DeNitrification and DeComposition, DNDC) was applied to predict nitrogen balance in cropland in 1998 at national scale. Data on climate, soil properties, cropping systems, acreage, and management practices at county scale were collected from various sources and integrated into a GIS database to support the model. The model results reveal that the simulated balance of N is net surplus in the whole country’s croplands in 1998 that range from 4.56 million t N to 9.62 million t N with an average of 7.09 million t N. Currently annual inputs of N mainly rely on the chemical fertilizer, and nearly 60% of N is input through fertilization. In terms of output of nitrogen in cropland, besides of the amounts uptake by plants growth, while nitrogen losses through volatilization of NH3 and leaching are the dominant occupying 35% and 15% of total output of N respectively, which will significantly affect the environment. The model results also indicate that the largest nitrogen surpluses distribute in the relatively developed provinces where the higher fertilizer are usually applied. Generally, it is urgent and necessary to hold back the inefficient losses of nitrogen.