Nitrogen (N) management is essential for food security. The North China Plain is an important food producing region, but also a hotspot of N losses to the environment. This results in water, soil, and air pollution. In this study, we aim to quantify the relative contribution of different crops and animals to N losses, by taking the Quzhou county as a typical example in the North China Plain. We developed and applied a new version of the NUtrient flows in Food chains, Environment, and Resource use (NUFER) model. Our model is based on updated information for N losses in Quzhou. Our results show that N losses to the environment from crop and animal production in Quzhou were approximately 9 kton in 2017. These high N losses can be explained by the low N use efficiency in food production because of poor N management. For crop production, wheat, maize, and vegetables contributed 80% to N losses. Ammonia emissions and N leaching have dominant shares in these N losses. Pigs and laying hens were responsible for 74% of N losses from animal production. Ammonia emissions to air and direct discharges of manure to water were the main contributors to these N losses. Effective reduction of N losses requires improving the nutrient management in crop (wheat, maize, vegetables) and animal (pigs, laying hens) production. Our work could support the Agricultural Green Development in the North China Plain.