<p>Excessive anthropogenic nitrogen emissions have severely disrupted nitrogen metabolism in cities, leading to serious ecological problems such as water eutrophication and biodiversity loss. The impact of urban nitrogen metabolism extends beyond physical boundaries, driven largely by human activities and inter-regional trade. Current urban metabolism studies focus on carbon, water, energy, and waste but lack a systematic understanding of nitrogen metabolism. This study integrates life cycle assessment (LCA), environmental extended multi-regional input-output model (EE-MRIO), ecological network analysis (ENA), and structural path analysis (SPA) to develop an integrated network model (LMES-INM). This model constructs urban nitrogen metabolism networks, tracks inter-regional nitrogen flows, identifies key nodes and paths, and quantitatively assesses multi-regional nitrogen metabolism networks. Using the Pearl River Delta (PRD) in China as a case study, we observed a declining trend in both direct and indirect nitrogen footprints. Most cities have higher indirect nitrogen footprints compared to direct ones, suggesting that ignoring the impact of indirect nitrogen emissions could increase the pressure on nitrogen reduction efforts. The nitrogen cycling network is primarily centered on the manufacture, followed by the services, with Foshan, Guangzhou, Zhongshan, and Dongguan’s manufacture, and Guangzhou and Shenzhen’s services being key representatives. The nitrogen cycling network gradually shifted from over-reliance on specific industries to a more balanced industrial structure. However, there are still significant competitive relationships within the network. The management of nitrogen emissions remains complex due to the intricate interactions between different cities and sectors. Further efforts are needed in government policy formulation and the support of complementary measures to enhance these collaborative nitrogen reduction initiatives.</p>