Abstract: Against the backdrop of global mangrove decline, China has achieved a net increase in mangrove coverage through ecological protection and restoration projects such as pond-to-mangrove conversion. To investigate the ecological impacts of pond-to-mangrove conversion on microbial communities in sedimentary environments, we focused on the pond-to-mangrove restoration area in Kaozhou Bay, Huidong County, Guangdong Province in 2021. Using high-throughput sequencing, we compared the distribution, specialist species, and environmental driving mechanisms of sediment microbial communities among mangrove-planted areas, mudflat and former aquaculture habitats. The results indicate that Desulfobacterota, Chloroflexota, and Pseudomonadota were the dominant microbial phyla shared among all three habitats. Although short-term mangrove restoration did not significantly enhance microbial α-diversity (p>0.05), it significantly increased β-diversity (p<0.05). Similarly, the former aquaculture site exhibited considerable vertical spatial heterogeneity of microbial communities, largely influenced by residual organic matters such as leftover feed and feces. In contrast, the mudflat site showed relatively uniform microbial composition along the sediment profile. A total of 60, 19, and 50 specialist species were identified in the mangrove, mudflat, and former aquaculture sites, respectively, whose distributions were significantly correlated with NH₃-N concentrations (In mangrove and mudflat sites) and particulate organic matter (POC, PON, and C/N ratio in the former aquaculture site). The findings help deepen the understanding of subsurface ecological recovery mechanisms during mangrove wetland restoration and provide a scientific basis for interpreting the ecological effects of land-use change.