Saline-alkali soil has poor fertility and low organic matter content, which are key factors that limit agricultural productivity. Intercropping systems can enhance biodiversity in farmlands, thereby increasing the organic matter content. During this process, soil microorganisms respond to environmental changes. Therefore, we conducted a three-year intercropping enhancement experiment using saline-alkali soil. To avoid nutrient and microbial differences caused by the varying nutrient demands of different crop types, we systematically sampled the tillage layer of the soil (0-20 cm) from the subsequent crop (wheat season) in the intercropping systems. We found that compared to the control group, the three intercropping systems significantly increased the nutrient content in saline-alkali soil, including total nitrogen, total phosphorus, total potassium, organic matter, available nitrogen, and available potassium. Notably, there were significant increases in total nitrogen, organic matter, and available potassium. The intercropping systems had varying effects on the alpha and beta diversities of soil bacteria and fungi. Specifically, the effect of intercropping on fungal alpha diversity was significantly greater than that on bacterial alpha diversity, whereas its effect on bacterial beta diversity was greater than that on fungal beta diversity. Additionally, intercropping influenced microbial community composition, increasing the abundance of and and decreasing the abundance of . It also increased the abundance of and and decreased the abundance of . Total nitrogen and soil organic matter were identified as the primary environmental factors that significantly affected bacterial community composition; however, they had no significant impact on fungal communities. Intercropping had different effects on the fungal and bacterial networks. It increased the stability and complexity of the bacterial network. However, although it improved the stability of the fungal network, intercropping reduced its complexity. In summary, intercropping with leguminous plants is an effective way to enhance soil nutrients, particularly organic matter, in saline-alkali soils. Simultaneously, intercropping affects the soil microbial community structure of subsequent crops; however, the responses of bacteria and fungi to intercropping are significantly different. The results of this study provide data support for improving saline-alkali land through planting systems.