Abstract: The crop-livestock system in Baiyangdian Basin has changed significantly owing to the implementation of related policies and establishment of the Xiong’an New Area. Based on the NUFER (Nutrient flows in Food chains, Environment and Resources use) model and data from statistical year books, surveys, and literatures, this study determined the nitrogen and phosphorus requirements for crop-livestock systems and analyzed the temporal and spatial characteristics of nutrient use and environmental losses in Baiyangdian Basin on a county scale in the years 2005, 2015, and 2018. The results showed that the inputs of nitrogen and phosphorus fertilizers in Baiyangdian Basin in 2018 were far less than those in 2005 and 2015. For example, the input of nitrogen fertilizer in 2018 was 8.0% and 11.6% lower than that in 2005 and 2015, respectively. The nitrogen use rate of the crop system remained at approximately 44% throughout the study period, whereas the phosphorus use rate increased from 27.1% to 30.7%. The total nutrient input and manure nutrient losses decreased significantly in the livestock system, especially for the directly discharge pathway, whose nitrogen and phosphorus losses reduced to 24.7 Gg and 10.3 Gg, respectively in 2018, which were only approximately 37% of that in 2015. Nitrogen and phosphorus use rates increased significantly for the whole livestock system, reaching 23.3% and 18.6%, respectively in 2018. In 2018, the nitrogen and phosphorus inputs in the crop-livestock system were significantly lower than those in the previous two study years. However, the nitrogen and phosphorus use rates of the whole crop-livestock system first increased and then decreased during 2005–2018. Spatial analysis revealed that the nutrient input, output, and loss of the crop-livestock system were relatively lower in the eastern and western Baiyangdian Basin but higher in the middle areas compared to those in other areas. In conclusion, the goal of “zero increase” in fertilizer and optimization of manure management was achieved in Baiyangdian Basin, but the nutrient use rates of the crop-livestock system were still at a low level. There was an unbalanced development pattern of crop-livestock systems; some counties were characterized by high input, high loss, and low efficiency. In the future, the Baiyangdian Basin should deepen the policy of zero increase in fertilizer, continue to implement the action of recycling livestock waste, and distribute animals rationally to ensure a synergistically optimized crop-livestock system.