Abstract: Separation of crop and livestock production increases the risk of environmental pollution and the wastage of nutrient resources derived from crop-livestock systems. Integration of crop and livestock production is an important pathway for promoting nutrient cycling and reducing nutrient losses. Research on nutrient management at the basin scale can upscale agricultural production technologies from the farm scale to the basin scale and improve nutrient-use efficiency. Based on production optimization, the environmental threshold of the basin can be used as a bayonet to further reduce environmental nutrient losses. In addition, it is important to achieve higher nutrient efficiency and greater environmental emission reduction of crop-livestock production systems in a large area via nutrient management at the basin scale, which may also support the green development of agriculture. Taking the Yangtze River Basin as an example, this study reviewed the significance of nutrient management based on the integration of crop and livestock production at the basin scale with green development, nutrient management technologies based on the integration of crop and livestock production, and spatial optimization based on the environmental cost of the crop-livestock production system. In addition, the present study focuses on the nutrient management of crop-livestock production systems at the basin scale. Based on the present review, we found that there are a series of nutrient management technologies for crop-livestock systems in the Yangtze River Basin, and the promotion and application of these technologies via a bottom-up approach could further reduce nutrient losses and improve agricultural production efficiency. However, the nutrient losses of the crop-livestock system in some areas are too high and cannot be controlled within the environmental threshold only through technical improvement; it is also necessary to conduct spatial planning for crop-livestock systems via a top-down approach. Future studies on nutrient management of crop-livestock systems at the basin scale should include (1) characteristics and driving factors of nutrient flow and environmental emissions at the basin scale, (2) classification of vulnerable areas of nutrient losses at the basin scale, and (3) evaluation and optimization of crop-livestock systems based on vulnerable areas.