China's successful achievement of food security in recent decades has resulted in serious damage to the environment upstream of the agricultural sector, on farm and downstream. The environmental costs of this damage are not only agro-ecosystem function and the long-term sustainability of food production, but also bio-physical including human health with impacts at all levels from the local to the global, and with economic loss estimates ranging from 7 to 10% of China's agricultural gross domestic product (GDP). This paper presents a systematic analysis of the causes and impacts of these environmental costs for China's cropping systems and crop-based livestock systems, and focuses on the nitrogen management. Since the 1980s most of the environmental costs have been related to the intensification of first grain production stimulated by high nitrogen fertilizer and irrigation subsidies, and then vegetable production and fruit trees, with the overuse and misuse of synthetic nitrogen fertilizer and manure being the dominant cause of eutrophication, soil acidification and high greenhouse gas emissions. However, during the last 10 years or so the expansion of intensive livestock production has become a serious cause of direct and indirect air and water pollution and is destined to be the main agricultural threat to China's environment in the long-term unless a holistic strategy for sustainable intensification is adopted for the next and future 5 Year Plans. This strategy should focus on improving nutrient management to limit nitrogen overuse, which is now the main cause of the economic losses from agriculture's damage to the environment.
