Abstract: To meet the increasing demand for food, the crop-livestock production system has developed rapidly. Meanwhile, it is also becoming the main source of nitrogen losses, but there are significant differences in the characteristics of environmental risks from nitrogen losses among different regions. Therefore, the precise optimization and regulation of crop-livestock production system by zones according to the spatial differences is of great significance to the sustainable development of China’s crop-livestock industry in the future. In view of this, this paper regulates nitrogen losses in Jing-Jin-Ji Region by partition and step-by-step optimization. Partition optimization mainly considers selecting corresponding emission reduction technologies based on the risk characteristics of nitrogen losses in different regions, and step-by-step optimization is mainly achieved through three steps, which were 1) integration of crop and livestock production (returning of organic fertilizer to the field according to the fertilizer demand for crop), 2) emission reduction technologies for different stages and different systems, and 3) spatial optimization by transferring livestock production from the areas with high level of nitrogen losses risk to the areas with no risk. Through the above methods, the risk of nitrogen losses in crop-livestock production system in Jing-Jin-Ji Region can be more precisely controlled, and the sustainable development in crop-livestock production system via effective nitrogen management can be achieved. The results of this study were showed as below. Through partition and step-by-step optimization in crop-livestock production system of Jing-Jin-Ji Region, the risk of environmental losses derived from nitrogen losses from crop-livestock production system can be reduced. For the risk due to ammonia emissions, the proportion of areas with medium- and high-level risk decreased by 30.81% after the first step of optimization, then decreased by 55.81% after the second step of optimization, and finally decreased by 58.42% after the third step of optimization. In the end, the proportion of number of counties and districts with low-level or no risk in Jing-Jin-Ji Region increased to 90.37%, and it indicates effectively reduction of the risk due to ammonia emissions in this region. For the risk due to nitrate losses, the proportion of area with medium- and high-level risk increased by 7.99% after the first step of optimization, then decreased by 22.20% after the second step of optimization, and finally decreased by 26.54% after the third step of optimization. In the end, the proportion of area of counties and districts under low-level risk or no risk in Jing-Jin-Ji Region increased to 83.85%. Therefore, the nitrogen management level of the crop-livestock production system in Jing-Jin-Ji Region can be significantly improved through precise regulation via partition and step-by-step optimization. Based on above, the promotion and application of nitrogen management in crop-livestock production system via partition and step-by-step optimization at regional level are of great significance to the green and sustainable development of crop and livestock production system with lowest economic inputs in the future.