Abstract: The integration of crop and livestock production promotes agricultural green development under the guarantee of food security in Black Soil Region in Northeast China. In this study, Nong’an County, Jilin Province, located in Black Soil Region in Northeast China, was selected as the study boundary. Quantitative studies for nitrogen and phosphorus flows, utilization efficiency as well as environmental losses in crop-livestock systems from 1990 to 2020 were conducted through field research, statistical data and literature, combined with the NUFER model (NUtrient flows in Food chains, Environment and Resources use). Explore the driving role of climate and socio-economic factors on nitrogen and phosphorus emissions. Furthermore, two scenarios of balanced fertilization (reduce fertilizer application) and organic substitution (increase organic material substitution) were set up to assess the county’s emission reduction potential. The results showed that, compared to 1990, nitrogen and phosphorus inputs to crop-livestock systems for Nong’an County in 2020 decreased by 41% and 20%, respectively, with chemical fertilizer application as the largest input. The nutrient utilization efficiency of crop system and crop-livestock systems increased fluctuatingly, while nutrient utilization efficiency of livestock system decreased and tended to remain stable. The nitrogen and phosphorus losses of crop-livestock systems decreased by 41% and increased by 29% compared to 1990, respectively. Ammonia volatilization from farmland, runoff and erosion, and livestock manure discharge as the major emission routes. Through balanced fertilization and organic substitution, it is predicted that by 2030, Nong’an County will have the potential to reduce the application of chemical nitrogen fertilizer by 70% to 80% and chemical phosphorus fertilizer by 80% to 85%, based on the low levels of soil nitrogen and phosphorus accumulation, and the environmental emissions will be reduced by 67%, the nutrient utilization efficiency of crop system and crop-livestock systems will increase by more than 50%. In conclusion, Nong’an County has a high application of chemical fertilizer and a significant waste of organic materials in crop-livestock systems, which resulted in a low level of nutrient utilization and high environmental emissions. In the future, increasing the potential of fertilizer application reduction is considerable by increasing the amount of crop straw and manure returned to the field. The Black Soil Region in Northeast China should continue to deepen the policy of zero grow in fertilizer, and promote the resource utilization of organic waste to guarantee a synergistically optimized crop-livestock systems.