Objective This study aimed to investigate the effects of intercropping Carya cathayensis Sarg. with Polygonatum cyrtonema Hua on composition, structure, and potential functions of soil bacterial community in C. cathayensis Sarg plantations, thereby providing a microbiological basis for their sustainable management.

Methods Soil samples from both rhizosphere and bulk were collected from two cultivation systems: C. cathayensis Sarg monoculture (C) and C. cathayensis Sarg–P. cyrtonema Hua intercropping (CP). Bacterial community composition and structure were analyzed using high-throughput sequencing, and functional profiles were inferred through predictive methods. The relationships between bacterial communities and soil chemical properties were further explored using redundancy analysis.

Results Intercropping significantly altered the structure and potential functions of soil bacterial communities. Specifically, the relative abundance of Acidobacteriota increased by 61.95% in rhizosphere soil and 18.34% in bulk soil, whereas Actinobacteriota decreased by 35.86% and 27.08%, respectively. At the genus level, Bradyrhizobium increased significantly by 26.88% in intercropped rhizosphere soil. Biomarker analysis revealed that Flavobacterium was enriched in intercropped soils, while Formylgalactosideaceae was more abundant under monoculture. Non-metric multidimensional scaling (NMDS) demonstrated significant separation of bacterial community structures between the two treatments (p<0.05). Co-occurrence network analysis indicated that intercropping reduced bacterial network complexity. However, functional predictions indicated increased abundances of microbial groups associated with nitrogen fixation, anaerobic heterotrophy, organic matter degradation, and urea decomposition. Furthermore, Methylomirabilota and Verrucomicrobiota were significantly correlated with soil alkali-hydrolyzable nitrogen and organic matter, respectively. Available phosphorus, available potassium, and organic matter were identified as key drivers of bacterial community variation.

Conclusion Intercropping with P. cyrtonema modified the soil microenvironment in C. cathayensis Sarg plantations, reshaping bacterial community structure, and enhancing microbial functions related to nutrient cycling and organic matter decomposition. However, the reduced bacterial network complexity during the early stage of intercropping suggests potential short-term shifts in microbial interactions. Long-term studies are required to elucidate microbial succession dynamics and to optimize understory management strategies for sustainable agroforestry systems.