【Objective】Cover crops are very important for regulating soil structure and enhancing soil organic carbon. Cover crops can improve soil pore structure by creating biopores through root penetration and subsequent decomposition. However, the effects of different cover crops on organic carbon accumulation and microbial communities in biopore sheaths remain unclear. 【Method】A field experiment was conducted in a typical Shajiang black soil, including four winter cover crop treatments (fallow, alfalfa, rapeseed, and a mixture of radish + hairy vetch) in rotation with summer maize. Soil organic carbon (SOC) and total nitrogen (TN) contents in the biopore sheaths of the 20–40 cm soil layer under different treatments were determined, while bacterial and fungal community structures were analyzed via high-throughput sequencing. 【Result】The results showed that, compared with bulk soil, SOC content in the biopore sheaths increased significantly by 33.4% under the alfalfa treatment, while TN content increased significantly by 24.6% and 18.5% under the alfalfa and radish + hairy vetch treatments, respectively. However, no significant differences in SOC and TN contents of the biopore sheath were observed among different cover crops. The microbial community structure varies significantly with the interaction between cover crop species and soil habitats. The bacterial α-diversity indices and niche breadth indices in biopore sheaths were significantly higher than those in bulk soil, particularly in the radish + hairy vetch treatment, whereas no significant differences were observed in fungal communities between the two soil compartments. Furthermore, microbial communities within biopore sheaths exhibited a shift toward copiotrophic taxa compared with bulk soil. The relative abundance of Pseudomonas and Bacillus was higher in alfalfa-derived biopore sheaths than in other treatments. Correlation analysis indicated that the relative abundance of core microbial taxa involved in carbon decomposition and transformation was significantly positively correlated with SOC content. 【Conclusion】In summary, SOC and TN contents in the biopore sheaths under the alfalfa treatment significantly increased. SOC content may regulate microbial community structures within biopore sheaths by influencing bacterial α-diversity indices, niche breadth indices, and the relative abundance of core microbial taxa.