To investigate the effects of long-term elevated atmospheric CO₂ (eCO₂) on the distribution and stability of soil aggregates and microbial characteristics in wetland soils and to reveal the mechanisms by which eCO₂ influences soil organic carbon (SOC) sequestration, a multi-temporal-scale eCO₂ control experiment was conducted in the Sanjiang Plain wetland with treatments at ambient CO₂ concentration (AC), 550 ppm, and 700 ppm CO₂. Soil aggregate fractionation, phospholipid fatty acid (PLFA) analysis, and redundancy analysis (RDA) were used to analyze changes in aggregate size distribution, stability indices (MWD, GMD), microbial biomass, and community structure. The results showed that eCO₂ significantly affected aggregate size distribution. Both short- and long-term exposure to low-concentration eCO₂ reduced the proportion of large aggregates. Over time, the proportion of silt and clay particles increased, while microaggregates decreased. Although CO₂ concentration did not directly affect MWD and GMD, long-term eCO₂ significantly reduced soil aggregate stability. Microbial biomass and diversity were not sensitive to CO₂ concentration but decreased significantly with prolonged exposure. In contrast, microbial community structure was significantly affected by both CO₂ level and exposure duration. RDA indicated that, under short-term eCO₂, aggregate fractions were positively correlated with microbial biomass, whereas, under medium- and long-term treatments, they were positively correlated with soil physicochemical properties. Macroaggregates were positively correlated with aggregate stability, while microaggregates and silt–clay fractions were negatively correlated—a relationship that strengthened with longer eCO₂ exposure. Thus, long-term eCO₂ altered soil aggregate structure and microbial communities, ultimately influencing SOC stability. These findings provide data and theoretical support for predicting soil carbon stability and ecosystem functioning in wetlands under climate change.