Abstract: The North China Plain faces a series of topsoil degradation issues—including reduced soil biodiversity, impeded nutrient transformation, decreased organic carbon and nitrogen content, and deteriorated soil structure—due to 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 during the 2022 maize season to compare monoculture maize with maize intercropped with a legume (Fendou Mulv No. 2, a forage-green manure variety). This study investigated the effects of long-term nitrogen (N) application rates combined with legume intercropping on soil aggregate composition, stability, and the distribution of organic carbon (SOC) and total nitrogen (TN) within aggregates. The aim was to clarify how interspecific and root–soil interactions in the 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 N application levels: 0 (N0), 100 (N100), 200 (N200), 300 (N300), 400 (N400), and 600 kg N ha^-1 (N600). During the maize grain-filling stage in September 2024, rhizosphere and non-rhizosphere soil samples were collected to analyze aggregate composition, SOC, and TN content. The results showed that fertilization had a weaker influence on aggregate composition and stability than cropping patterns. Significant changes in fragmentation and stability rates of coarse macroaggregates (≥2 mm) were observed only in the rhizosphere of intercropped maize (FM). No significant differences were detected across N treatments in the rhizosphere of the legume (F), monocropped maize (M), or bulk soil (B). Across all N levels, the rhizosphere soils (FM, F, M) showed reduced fragmentation and increased stability of coarse macroaggregates (≥2 mm) compared to non-rhizosphere soil. Intercropping reduced the fragmentation rate and increased the content of water-stable macroaggregates in the maize rhizosphere, with the highest stability (39.3%) occurring under the N400 treatment, indicating that appropriate N application improves aggregate stability in intercropping systems. Nitrogen application enhanced SOC and TN content, but the extent of increase differed between intercropping and monoculture under high N inputs. Intercropping was more beneficial for increasing soil carbon and nitrogen under low-N conditions. SOC and TN were mainly stored in macroaggregates, particularly in fine macroaggregates (0.25–2 mm), which contributed 54.8%–77.0% of SOC and 60.6%–69.3% of TN. Intercropping increased SOC and TN content within macroaggregates, most notably in coarse macroaggregates, suggesting that changes in cropping practice first affect the distribution of carbon and nitrogen in larger aggregates. In conclusion, maize-legume intercropping enhances the content and stability of macroaggregates, increases SOC and TN sequestration, and promotes the physical protection of soil organic matter.