Eucalyptus is one of the most important fast-growing tree species for afforestation with economically significance. But its adverse ecological effects of successive planting of Eucalyptus plantation have caused controversy, including soil degradation, reduced plant diversity and stand productivity. To ensure their sustainability remains an important topic in forestry. However, our understanding about the effects of Eucalyptus on composition and functions of soil microbial community remain poorly understood. Understanding these impacts is crucial to provide a basis for silvicultural management to address the adverse ecological effects on Eucalyptus plantations. In order to characterize the dynamics of different microbial categories, such as fungi, bacteria and archaea, a chronosequence of Eucalyptus plantations of 2, 7, 12, 17, and 22 years were selected. The metagenomic sequencing was used to measure the response of microbial community structure, diversity, and function in both rhizosphere and bulk soil of Eucalyptus plantations across different ages. The results suggested that there was a pattern of initial decline followed by an upswing in soil physicochemical properties and diversity with stand age. At 12 years, the fungal communities in rhizosphere soil showed the lowest diversity. Meanwhile, both archaea communities in the rhizosphere and bulk soil, as well as bacteria communities in the bulk soil, had their lowest diversity at 7 years, respectively. The composition of microbial communities between rhizosphere and bulk soil significantly differed across different stand ages. Interestingly, stand age did not induce significant shifts in the dominant fungal genus between rhizosphere and bulk soil, which was identified as Rhizophagus. However, the significant changes in the dominant genera of both bacterial and archaeal in rhizosphere soil were detected. The prevailing bacterial groups were identified as Bradyrhizobium and Bacteroides, while the dominant archaea were identified as Candidatus-Nitrosotalea and Methanocorpusculum. The nitrate nitrogen significantly influenced the composition and diversity of fungi, while pH significantly influenced bacterial and archaeal diversity and community composition. Additionally, soil phosphorus availability was another major driving factor for archaeal diversity and community composition. There were significant differences in the functional profiles of fungi, bacteria, and archaea between rhizosphere soil and bulk soil. Meanwhile, the bacterial community tended to be more variable than fungi and archaea. This study illustrated the dynamic response of soil microbial communities in both rhizosphere and bulk soil across a chronosequence of Eucalyptus plantations. The results emphasize the impacts of stand age on soil physicochemical properties and dynamics of microbial communities. The findings are with important implications for sustainable management of soil microorganisms, improving the productivity and multi-functional management of Eucalyptus plantations.