Abstract: Crop-livestock production system has developed rapidly to meet the increasing demand of food. However, it is also becoming the main source of nitrogen losses, and 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 zone according to spatial differences are of great significance to the sustainable development of the crop-livestock industry in China in the future. Therefore, this study involved the regulation of nitrogen losses in the Jing-Jin-Ji Region via partitioning and step-by-step optimization. Partition optimization mainly considers the selection of 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: 1) integration of crop and livestock production (returning of organic fertilizer to the field according to the fertilizer demand for crops), 2) emission reduction technologies for different stages and different systems, and 3) spatial planning via the transfer of livestock production from areas with medium- and high-level risk to areas with low-level and 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 sustainable development in crop-livestock production system via effective nitrogen management can be achieved. The results of this study were as follows: Through the partitioning and step-by-step optimization of crop-livestock production system in Jing-Jin-Ji Region, the risk of environmental losses derived from nitrogen losses from crop-livestock production system can be reduced. Regarding the risk caused by ammonia emissions, compared to baseline scenario in Jin-Jin-Ji Region in 2017, the proportion of administrative areas (same as below) with medium- and high-level risks decreased by 30.81% after the first step of optimization, then totally decreased by 55.81% after the second step of optimization, and further totally decreased by 55.94%–58.42% after the third step of optimization. In the end, the proportion of the administrative areas with low-level or no risk in the Jing-Jin-Ji Region increased to 87.89%–90.37%, indicating effective reduction in the risk caused by ammonia emissions in this region. Regarding the risk caused by nitrate losses, compared to baseline scenario in Jin-Jin-Ji Region in 2017, the proportion of areas with medium- and high-level risks increased by 7.99% after the first step of optimization, then totally decreased by 22.20% after the second step of optimization, and further totally decreased by 22.19%–26.54% after the third step of optimization. Ultimately, the proportion of administrative areas under low-level risk or no risk in the Jing-Jin-Ji Region increased to 79.50%–83.85%. The nitrogen management level of the crop-livestock production system in the Jing-Jin-Ji Region can be significantly improved through precise regulation via partitioning and step-by-step optimization. Therefore, the promotion and application of nitrogen management in crop-livestock production systems via partitioning and step-by-step optimization at the regional level are of great significance for green and sustainable development of crop-livestock production system with very low economic inputs in the future.