The invasion of alien plants has significant implications for vegetation structure and diversity, which could lead to changes in the carbon (C) input from vegetation and change the transformation and decomposition processes of C, thereby altering the dynamics of soil organic carbon (SOC) within ecosystems. Whether alien plant invasion increases the SOC stock and changes SOC fractions consistently within regional scales, and the underlying mechanisms driving these SOC dynamics remain poorly understood. This study investigated SOC dynamics by comparing the plots that suffered invasion and non-invasion of Solidago Canadensis across five ecological function areas in Anhui Province, China, considering climate, edaphic factors, vegetation, and soil microbes. The results demonstrated that the impact of S. Canadensis invasion on SOC storage was not consistent at each site in the 0–20 cm soil layer, as indicated by the range of SOC content (5.94–12.45 g kg−1) observed at non-invaded plots. Stable SOC exhibited similar response patterns with SOC to plant invasion, whereas labile SOC did not. In addition, bacterial and fungal communities were shifted in structure at each site by plant invasion. Bacterial communities exhibited greater resistance to S. Canadensis invasion than did fungal communities, as evidenced by three aspects of the resistance indices—community resistance, phylogenetic conservation, and network complexity. The mechanisms driving SOC dynamics under S. Canadensis invasion were explored using structural equation models. This revealed that fungal keystone taxa responsible for community resistance controlled stable SOC fractions. In contrast, bacterial keystone taxa had the opposite effect on labile and stable SOC. Climatic and edaphic factors were also involved in the labile and stable SOC dynamics. Overall, this study provides novel insights into the dynamics of SOC under S. Canadensis invasion on a regional scale.