Available information on interaction mechanisms between soil nutrient stoichiometry and microbial communities associated with soil aggregate structure in restored wetlands remains limited. As such, this study investigated water-stable aggregate structure using wet-sieving method and scanning electron microscope (SEM) in restored wetlands with a restoration duration of 0, 1, 2, 3, 5, 13 or 19 years, and their internal nutrient stoichiometry and microbial communities (phospholipid fatty acid analysis, PLFAs). The results showed that soil aggregate structure tended to be stable from the fifth restoration year. In the restored wetlands, General bacteria, Gram-positive bacteria (G(+)), and Gram-negative bacteria (G(-)) were the dominant components of soil microorganisms, which tented to condense in coarse-aggregates. The carbon-to-phosphorus (C:P) and nitrogen-to-phosphorus (N:P) ratios were higher in coarse-aggregates since C and N benefit from the physical protection. Redundancy analysis (RDA) results indicated that C:N ratio was primary environmental factors controlling the distribution of soil microbial communities. In the Sanjiang Plain, the soil organic carbon (SOC) decomposition was lower, and N was the primary nutrient limiting wetland restoration quality.