Intercropping is considered a sustainable practice because it is environmentally friendly and can result in high yields, while decreasing nitrogen (N) applications is considered an effective way to reduce greenhouse gas emissions in agricultural systems. However, exactly how intercropping and reduced nitrogen applications affect symbiotic arbuscular mycorrhizal fungi (AMF) in the roots and soils of intercropped maize/soybean plants cultivated in South China remains unknown. Thus, we evaluated the diversity, composition, and structure of the arbuscular mycorrhizal fungal community in the roots, rhizosphere and the bulk soils of maize (Zea mays) and soybean (Glycine max) with no nitrogen fertilization (N0), reduced nitrogen fertilization (N1), and conventional nitrogen fertilization (N2) in a sweet maize/soybean strip intercropping system (S2B4) and in monocultures (SB or SS) during a 4.5-year period (2013–2017, for a total of 9 cropping seasons). We classified 120 operational taxonomic units based on Miseq sequencing data, including one phylum, 7 families, 7 genera, and 25 virtual species. Arbuscular mycorrhizal fungal colonization was lower only in the roots of soybean associated with the intercropping system (S2B4) under no fertilization (N0) than in those in other treatments. Glomus was the most predominant genus in the roots and soil in both monocultures and intercropping systems among the N0, N1, and N2 groups. Significantly higher diversity and co-occurring species were observed in the N0 group than in the N1 and N2 groups, and significant differences in the community structure were found in all treatments. Moreover, the pH, soil organic matter, available nitrogen, ammonium nitrogen, nitrate nitrogen (NO₃-N), and available phosphorus (AP) were the main driving forces shaping the arbuscular mycorrhizal fungal community in maize rhizosphere and bulk soils, whereas only the pH influenced the arbuscular mycorrhizal fungal community in soybean soils. In conclusion, both nitrogen application and intercropping influenced the arbuscular mycorrhizal fungal community composition and structure, but nitrogen application had a stronger influence than cropping pattern on the arbuscular mycorrhizal fungal community diversity in the maize/soybean strip intercropping systems; moreover, pH, NO₃-N, and AP were the main factors driving the arbuscular mycorrhizal fungal community structure.