Soybean is a vital crop, serving as a significant source of vegetable oil and protein. However, soybean mosaic virus (SMV) is a widespread pathogen that adversely affects soybean yields globally. This research provides an essential step towards understanding the effects of intercropping soybean varieties with maize and varying planting densities on SMV incidence, its relationship with aphid population, and the resulting impact on soybean crop productivity. The study was conducted over two seasons and included nine treatments, combining three soybean cultivars (Giza 21, Giza 82, and Giza 111), three planting densities (low, mid, and high), and intercropping or sole plantings. The DAS-ELISA test was employed to detect SMV, while aphid populations were monitored weekly. Jasmonic acid content was quantified, and SDS-PAGE was used to assess the synthesis of novel proteins influenced by intercropping and planting density. Agronomic traits and seed productivity were also measured, and data were analyzed using ANOVA. The results demonstrated that intercropping decreased the percentage of SMV by 48.24% and 49.12% in the first and second seasons, respectively, compared with sole ones. Moreover, high plant density reduced SMV incidence in Giza 21 and Giza 111, while the reverse was true for Giza 82. SMV incidence was highly correlated with aphid population for cultivar Giza 82 compared with the other cultivars under intercropping or sole plantings. This study recommends planting the Giza 111 soybean cultivar with high plant density, as it showed a low rate of SMV infection, tolerance to aphid infestation, and high seed productivity under intercropping.