Abstract: Current studies on soil microorganisms in the black soil regions of Northeast China have predominantly focused on surface soils, resulting in a limited understanding of deep soil microbial communities, and their ecological functions in carbon and nitrogen cycles remain unclear. To reveal the ecological characteristics of soil microbial communities at different depths in a representative black soil region of Northeast China, we collected soil samples from various depths across representative habitat types in the region, and employed 16S rRNA gene amplicon sequencing to analyze the ecological features of microbial communities. The results showed that soil depth was the primary driver of bacterial community differentiation in black soils, while habitat type exerted a secondary modifying effect; soil bulk density (SBD) and total carbon (TC) were the key physicochemical factors shaping community structure. The surface layer was enriched in copiotrophic groups such as Proteobacteria, whereas the deep soil layer was dominated by oligotrophic groups including Chloroflexi, Acidobacteriota, and unique archaea. Canonical correlation analysis (CCA) revealed that TC and total nitrogen (TN) were positively correlated with bacterial communities, while SBD showed a significant negative correlation with the communities. These three factors collectively drove community differentiation through vertical and spatial heterogeneity. Habitat type exerted secondary modification on the depth-dominated community pattern: forestlands maintained high microbial diversity, anthropogenic disturbance in dry farmlands caused soil degradation and reduced community diversity, and water management in paddy fields reshaped the vertical distribution pattern of microorganisms. This study clarifies the core driving mechanism of vertical differentiation of black soil microbial communities and provides molecular indicators for microecological diagnosis of black soil degradation. We recommend that deep soil microbial characteristics be incorporated into the black soil health evaluation system.