The environmental emission of nitrogen (N) permeates through the entire food chain and ecological system. Nitrogen-efficient technologies in crop or livestock production alone have proven ineffective in controlling N pollution, necessitating the innovation of systematic research and management methods. A new framework, CAFE, that defines four N management systems (Cropping system, Animal-crop system, Food system, and landscape Ecosystem) hierarchically, has been established to quantify N flow to a broader perspective and help understand the complex dynamics and interactions across different N cycle systems. CAFE can be applied globally for different regions, helping elucidate the differences of N management levels in various regions and providing a new perspective and methodology for global sustainable N management. Applying CAFE to 13 representative countries reveals that the N surplus in most countries increased and the NUE decreased with the increase of the level of managed system. The N surplus in the animal-crop system, food system, and regional ecosystem increased by 152% (median), 230%, and 287%, respectively, based on the cropping system. The N surplus eventually increased from 3-153 kg·hm-2 in the cropping system to 63-464 kg·hm-2 in the regional ecosystem. At the same time, NUE decreased from 55% (median) in the cropping system to 30% in the animal-crop system and 18% in the food system. N loss increases gradually from crop production to primary agricultural products, food production, and consumption. Although the trend of N surplus increase is consistent across all countries, the magnitude of the increase varies considerably among countries, determining the different priorities for improving N management in each country. For China, as the high nitrogen surplus mainly comes from the cropping system, efforts need to be made to reduce the N surplus in cropland by promoting best management practices and adjusting the structure of N inputs. For most Western countries, the system outside the cropland contributes more to the total N surplus, and attention should be given to the N recycling of related systems. For example, the Netherlands needs to focus on matching crop-livestock structure, increasing feed self-sufficiency rate, and reducing livestock density to decrease N surplus in the animal-crop system. Japan needs to further reduce food waste or increase circulation, while African countries need to reduce crop storage waste and improve overall productivity. The analysis of the global CAFE system shows that the main factors affecting the surplus increment across systems include the structure of N input in cropland, livestock density, feed self-sufficiency rate, and the relationship between food trade and domestic supply and demand. However, these factors have not yet received attention in global N management. CAFE provides a consistent quantitative method for global N whole-chain management, which is helpful for cross-regional comparison, experience sharing, and policy formulation.