Abstract: With the rapid development of agriculture and animal husbandry, large nitrogen inputs have caused a series of environmental problems. To provide a scientific reference for regional nutrient management, Jiangsu Province, an economically developed region in the Yangtze River Delta, was selected to study the nitrogen flow characteristics in crop-livestock systems from 1998 to 2018 and their environmental effects. The research was based on the NUFER model (NUtrient flows in Food chains, Environment and Resources use, NUFER) and incorporated statistical yearbook data, survey data, and literature data. The nitrogen account balance, nitrogen use efficiency, nitrogen recycling, and loss of the crop-livestock systems in Jiangsu Province were quantitatively analyzed, and the relationships between the economy, resources, and environment of the crop-livestock systems were explored based on a structural equation model. The results showed that from 1998 to 2018, the crop subsystem increased the amount of nitrogen carried by the crop products under the gradual decrease of the total nitrogen imports of the subsystem. Nitrogen carried by the main crops and crop by-products increased from 8.31×10⁵ t to 1.20×10⁶ t. Total nutrient loss also declined. For the livestock-poultry subsystem, nitrogen was mainly introduced via exogenous and local feed; exogenous feed was the main source of nitrogen in the subsystem. The proportion of local feed nitrogen supply increased annually, from 29.32% in 1998 to 44.77% in 2018. From 1998 to 2018, the nitrogen use efficiency of the crop-livestock system increased from 21.39% to 35.00%. The amount of straw to field, local feed, and manure to field increased annually, and the total amount of recycled nitrogen increased from 2.54×10⁵ t to 3.00×10⁵ t. Nitrogen environmental emissions decreased in the past 20 years, and the main sources of loss included soil nitrogen surplus, gas emission loss, water discharge loss, and manure residue. The structural equation model results showed that in the developmental process of the agricultural and animal husbandry systems in Jiangsu Province, economic development and resource reduction promoted improvements in product output and system efficiency. Under the guidance of regional development and policies, crop-livestock systems in Jiangsu Province developed rapidly from 1998 to 2018. The scale of the agricultural and animal husbandry systems had continuously expanded, resource utilization had been relatively efficient, and environmental emissions had gradually decreased. However, there was also a slight imbalance in the development of crop-livestock systems, and there were relatively few combinations of crop-livestock. Future development of the agriculture and animal husbandry systems in Jiangsu Province should focus on coupling the crop and animal husbandry subsystems, moderately expanding the production scale, and balancing the development of agriculture and animal husbandry subsystems to promote local agriculture and animal husbandry.