Mangrove wetlands are highly productive ecosystems in tropical and subtropical coastal zones, play crucial roles in water purification, biodiversity maintenance, and carbon sequestration. Recent years have seen the implementation of pond return initiatives, which have facilitated the gradual recovery of mangrove areas in China. However, the implications of these initiatives for soil aggregate stability, microbial community structure, and network interactions remain unclear. This study assesses the impacts of converting ponds to mangroves—both in natural and artificially restored settings—on soil aggregate stability and microbial networks at typical mangrove restoration sites along China's southeastern coast. Our observations confirmed our hypothesis that pond-to-mangrove conversions resulted in an increase in the proportion of large aggregates (>0.25 mm), improved soil aggregate structural stability, and increased carbon sequestration. However, mangrove recovery led to a decrease in the abundance and diversity of soil fungi communities. In terms of co-occurrence networks, naturally restored mangrove wetlands exhibited more nodes and edges. The naturally recovered mangrove wetlands demonstrated a higher level of community symbiosis compared to those that were manually restored. Conversely, bacterial networks showed a different pattern, with significant shifts in key taxa related to carbon sequestration functions. For instance, the proportion of bacterial Desulfobacterota and fungi Basidiomycota in natural recovery mangrove increased by 15.03 % and 7.82 %, respectively, compared with that in aquaculture ponds. Soil fungi and bacteria communities, as well as carbon sequestration by aggregates, were all positively correlated with soil total carbon content (P < 0.05). Both bacterial and fungal communities contributed to soil aggregate stability. Our study highlights the complex relationships between soil microbial communities, aggregate stability, and the carbon cycle before and after land-use changes. These findings underscore the potential benefits of restoring mangrove wetlands, as such efforts can enhance carbon storage capacity and significantly contribute to climate change mitigation.