Abstract: The North China Plain faces a series of topsoil degradation issues, including reduced soil biodiversity, impeded nutrient transformation, decreased organic carbon and nitrogen contents, and deteriorated soil structure, owing to the high multiple cropping index, monoculture cropping, lack of fallow periods, and long-term emphasis on production over conservation in agricultural practices. Based on a long-term fertilization experiment initiated in 2003 in a wheat-maize rotation system at the Luancheng Agro-Ecosystem Experimental Station, Chinese Academy of Sciences, a split-plot design was implemented from the 2022 maize season to compare monoculture maize with maize intercropped with a legume (‘Fendoumulv No. 2’, a dual-purpose soybean variety for forage and green manure). This study investigated the effects of long-term nitrogen application combined with maize||soybean intercropping on soil aggregate composition, stability, and distribution of organic carbon (SOC) and total nitrogen (TN) within aggregates. This study aimed to clarify how interspecific and root-soil interactions in an intercropping system contribute to the physical protection of soil carbon and nitrogen, thereby supporting the development of green technologies that integrate land use with soil conservation. The experiment included six nitrogen application rates: 0 (N0), 100 (N100), 200 (N200), 300 (N300), 400 (N400), and 600 (N600) kg(N)∙hm⁻². During the maize grain-filling stage in September 2024, rhizosphere and non-rhizosphere soil samples were collected to analyze the aggregate composition and SOC and TN contents. The results showed that fertilization had a weaker influence on aggregate composition and stability than the cropping pattern. Significant changes in the fragmentation and stability rates of coarse macroaggregates (≥2 mm) were observed only in the rhizosphere soil of intercropped maize (FM). No significant differences were detected across the nitrogen application rates in the rhizosphere soils of the intercropped soybean (F) and monocropped maize (M), or bulk soil (B). Across all nitrogen application rates, rhizosphere soils (FM, F, and M) showed reduced fragmentation and increased stability of coarse macroaggregates (≥2 mm) compared to non-rhizosphere soils. Intercropping reduced the fragmentation rate in the maize rhizosphere soil, with the highest stability (39.3%) occurring under the N400 treatment, indicating that appropriate nitrogen application improved aggregate stability in intercropping systems. Nitrogen application enhanced the soil SOC and TN contents, but the extent of the increase differed between intercropping and monoculture under high nitrogen inputs. Intercropping was more beneficial for increasing soil carbon and nitrogen contents under low nitrogen conditions. SOC and TN were mainly stored in macroaggregates, particularly in fine macroaggregates (0.25−2 mm), which contributed 54.8%−80.0% of SOC and 60.6%−69.3% of TN. Intercropping increased the SOC and TN contents within macroaggregates, particularly in coarse macroaggregates, suggesting that changes in cropping practices primarily affect the distribution of carbon and nitrogen in larger aggregates. In conclusion, maize||legume intercropping enhanced the content and stability of macroaggregates, increased SOC and TN sequestration, and promoted the physical protection of soil organic matter.