Based on the 2002 field experimental results in the Wusi Farm of Fengxian County in Shanghai and related studies, and by the methods of ecological economy and environmental economy, this article examined and estimated the nitrogen input and output, and the economic values of nitrogen transformation in rice field ecosystems. The results indicated that the plot without N fertilization showed a deficit of nitrogen budget, while those with urea application showed a surplus. The economic value of the plot without urea amendment was evaluated to be positive, while that of the plots with urea application was calculated to be negative. The negative value of the plots with urea amendment resulted from the nitrogen losses through ammonia volatilization, nitrogen leaching and runoff, which had serious harmful impacts on environment and human society. Therefore, only when some measures were taken to encourage and facilitate farmers to improve the efficiency of urea application and to mitigate the environment problems from N losses in the process of food production, the advantages of nitrogen transformation in rice fields could be promoted, and the sustainability of agriculture would become reality.