Phosphorus (P) is a key limiting nutrient in crop-livestock production. Still, excessive application and inefficient utilization have made it the primary source of P pollution in China. Currently, there is a lack of systematic research on the contribution of P losses from city-scale crop-livestock systems to exceeding safe phosphorus planetary boundaries (PPB), coupled with a paucity of precise management strategies linked to water quality targets. We constructed a comprehensive P flow assessment framework by enhancing the NUFER (Nutrient flows in Food chains, Environment, and Resource use) model. This framework was used to systematically evaluate city-scale P flow characteristics and investigate the contribution of urban P losses to exceeding the PPB. Additionally, we identified P loss hotspots, revealed key drivers, and evaluated the mitigation potential of P losses under localized P management strategies. Analysis of temporal trends between 2000 and 2022 revealed that P losses initially increased before declining, peaking in 2005. The proportion of P losses surpassing the loose PPB threshold decreased from 98.28% to 42.59%. P loss hotspots are predominantly distributed across the Huang-Huai-Hai Plain, northern Middle-lower Yangtze River Region, central Sichuan Basin and Surrounding Regions, central-western Yunnan-Guizhou Plateau, central Loess Plateau, central-western Northeast China Plain, and central-eastern Northern Arid and Semiarid Region. The validation results confirmed that the P loss simulation results possess high reliability (P < 0.01, R-2 = 0.62). Livestock units (LU) emerged as the primary driver of P losses, with the interaction between LU and long-term average precipitation exerting the most pronounced influence. Scenario analysis indicates that integrated management measures, including crop fertilization recommendations, improving the efficiency of agricultural resource recycling, and adjusting livestock farming structures, could reduce P fertilizer inputs by 27.86% and P losses by 42.90%. Under localized P management strategies, P losses in China's crop-livestock systems are 28.08% below the loose PPB. The findings of this study provide a scientific basis for large-scale differentiated P management and water resource conservation strategies.