<p>Land use changes, especially urban land expansion, exert a profound effect on nitrogen (N) cycles in the interconnected human–natural systems, altering the distribution and intensity of N emissions resulting from anthropogenic activities. However, few studies have revealed the dynamic response of N emissions to diverse land use changes at the regional scale. This study developed a holistic spatial urban metabolism framework that combines land-use classification, N-flow modeling, and spatial analysis to examine the heterogeneous land-related N transitions across cities and timeframes at a fine spatial resolution. Using the Guangdong–Hong Kong–Macao Greater Bay Area (GBA) as the case, we observed a drastic expansion of built-up land during 1990–2018, mainly converted from cropland (81.35%) and forest (9.55%). Intensified N emissions became increasingly concentrated in densely populated urban areas and croplands in the GBA’s western peripheral cities. Land conversion from cropland to built-up land contributed the most to the rise in N emissions, totaling 368.2 Gg during the study period. The increase in N emission intensity associated with built-up land expansion gradually fell over time due to enhanced N removal in waste treatment, while the exploitation of water and wetland exhibited the highest average increased intensity of 35.01 t N/km² after 2010. Our findings highlight the need for tailored and collaborative land management strategies that adapt to different development stages and local conditions to mitigate N pollution in the fast-urbanizing bay area.</p>