Plants host diverse microbial communities essential for nutrient acquisition, growth, and responses to biotic and abiotic stresses. Despite their importance, the variation and stability of these communities during forest succession remain poorly understood. This study investigated the microbial communities in forests at different stand ages (12, 22, 30, and 40 years). Results showed that the phyllosphere and roots of harbor diverse microbial communities, which shift dynamically with forest aging. Bacterial species diversity consistently surpassed fungal diversity across all habitats. Forest aging significantly influenced the alpha diversity of phyllosphere and soil microbes, whereas root-associated microbial diversity remained stable. Co-occurrence network analysis revealed that bacterial communities formed more complex networks than fungal communities and exhibited greater stability. Functional annotation confirmed that bacterial communities were functionally more stable, predominantly involving metabolic processes. In contrast, endophytes dominated the phyllosphere fungi, while ectomycorrhizal fungi were prevalent in root and soil fungal communities. Environmental factors, including total nitrogen, total phosphorus, available potassium, and pH, emerged as key drivers of microbial dynamics. These findings provide novel insights into the differing responses of bacterial and fungal communities to forest aging, highlighting the critical role of ecological niches in shaping microbial dynamics.