With a rapid development and decoupling between crop and animal production, China already faces serious groundwater pollution by nitrate leaching, eutrophication of surface waters, as well as air quality degradation caused by over-fertilization and manure discharge. It is important to (1) quantify nutrient flows in "soil-crop-livestock" production system, (2) optimize nutrient flows and recycling by coupling crop and livestock systems, and (3) mitigate nutrient losses and improve nutrient use efficiency. These studies provide a scientific basis for national action (e.g. reduction of chemical fertilizer application, replacement of chemical fertilizer by manure, resource utilization of livestock waste and mitigation of non-point source pollutions). The objectives of this study are to review the published studies on nutrient management in crop and animal production, analyze the characters of nutrient inputs, use efficiencies and losses of crop and animal production in China in the past decades, and to prospect research priority of nutrient management in soil-crop-Animal production systems in China. For increasing productivities of grain, overuse of chemical fertilizer is common, lack of manure recycling. The biggest challenge facing China today is de-coupling crop and animal production. The nutrient use efficiency of crop and animal production decreased and nutrient losses increased dramatically in the past decades in China. The highest emissions are estimated in or around big metropolitans. Coupling crop and animal production is the main solution of sustainable intensive agriculture. According to the international research experiences, research should focus on improving manure management, mitigation of nutrient losses and increasing nutrients recycling rate of agricultural wastes. The integrated nutrient management of the soil-crop-Animal production systems has become the focus of global concern. Key research topics of nutrient management in crop and animal production include (1) quantifying nutrient flows and environmental impacts of 'soil-crop-Animal' production systems, (2) strategies of chemical fertilizer replacement by manure, (3) mitigation options of manure management from 'feeding-housing-storage-Treatment-Application' chain, and (4) farming system design for achieving high productivities and nutrient use efficiencies in crop and animal production.