【Objective】Due to the impacts of climate change and human activities, soil salinization has been increasingly intensified, posing a serious threat to food security and sustainable agricultural development. Cover crop planting, as a sustainable agricultural practice widely applied worldwide, has been proven to effectively enhance soil organic carbon (SOC) stocks; however, its mechanisms in saline-sodic soils, particularly the microbially driven processes, remain poorly understood.【Method】In this study, saline-sodic soils in the Songnen Plain were selected as the research object. Different salinity–alkalinity gradients were established, and maize monoculture and maize-Vicia villosa intercropping systems were implemented. The effects of cover crop intercropping on soil salinity-alkalinity characteristics, SOC fractions, microbial community structure, and microbial interaction networks were systematically analyzed to reveal the intrinsic mechanisms regulating SOC accumulation.【Result】The results showed that: (1) maize-Vicia villosa intercropping reduced soil electrical conductivity (EC), pH, and exchangeable sodium percentage (ESP), alleviated soil saline-alkali stress, and increased SOC and its fractions, especially mineral-associated organic carbon (MAOC); (2) maize-Vicia villosa intercropping promoted the enrichment of functional microbial taxa such as Nitrosomonadaceae and Nitrososphaeraceae by improving the soil saline–alkali environment, thereby enhancing nitrogen transformation potential; (3) microbial co-occurrence network analysis showed that maiz-Vicia villosa intercropping reduced network complexity but increased network stability, which may be conducive to the formation of a microbial interaction system more adaptive to saline-alkali stress; (4) random forest analysis revealed that MAOC was the most important predictor of SOC, and correlation analysis indicated that SOC was significantly positively correlated with MAOC and microbial biomass carbon (MBC) (P < 0.05), and significantly negatively correlated with EC, pH, and ESP (P < 0.05).【Conclusion】Under saline-alkali stress, soil organic carbon accumulation may depend primarily on specialist microbes rather than the entire community. Cover crop intercropping alleviates saline-alkali stress, thereby driving the restructuring of microbial communities and optimizing their interaction networks. This process promotes the transformation of organic carbon into stable carbon pools, ultimately facilitating the accumulation and sequestration of SOC.