[Objective] To study the composition, functional characteristics, and vertical distribution features of microbial communities of three different habitats in the Yellow River Delta wetland ecosystem, and provide theoretical support and potential microbial resources for targeted restoration and sustainable management of wetland ecology. [Methods] By using 16S rRNA gene amplicon sequencing and metabolomics analyses, we compared the composition and structures of soil bacterial communities in three habitats (vegetation-covered area, bare land, and biohabitat), and analyzed the characteristics of bacterial communities at varying soil depths as well as the potential interactions between habitat-specific bacteria and metabolites. [Results] The dominant phyla in the three habitats were Proteobacteria and Bacteroidota. The dominant phyla specific to the shallow and deep soil layers were Gemmatimonadota and Firmicutes, respectively. The unidentified MBNT15 in the vegetation-covered area, Halomonas in the bare land, and unidentified Rhodobacteraceae and Woeseia in the biohabitat showed significantly different abundance between different depths, and Bacillus was enriched in the deeper soil layer of all the three habitats. Metabolomic analysis revealed that the vegetation-covered area showed higher levels of sphinganine, 3-indoleacrylic acid, 2,4-dihydroxybenzoic acid, and perfluorooctanoic acid. Deoxycholic acid had the highest level in the bare land, while sulfamethoxazole was the highest in the biohabitat, which had lower level of l-tryptophan. Correlation analysis revealed that in the vegetation-covered area, Micrococcus luteus and Pseudomonas geniculata showed significantly positive correlations with sphinganine and perfluorooctanoic acid. Saccharospirillum salsuginis had significantly positive correlations with 3-indoleacrylic acid and 2,4-dihydroxybenzoic acid. In the bare land, Bacillus horikoshii showed a significantly positive correlation with deoxycholic acid. In the biohabitat, Halomonas ventosae had a significantly positive correlation with l-tryptophan, while Halomonas korlensis showed a significantly positive correlation with sulfamethoxazole. [Conclusion] Our study demonstrated that varying soil depths significantly impact the structure of microbial communities, and the structural and functional characteristics of soil microbial communities exhibit habitat specificity. The enriched bacteria such as M. luteus in the vegetation-covered area may promote plant growth and enhance stress resistance by regulating metabolites. The enriched Bacillus in the bare land plays a role in decomposing bird feces. The unique bacteria such as H. ventosae in the biohabitat demonstrate the potential for maintaining the ecological health of crab habitats through metabolite regulation. These findings offer new insights into the microbial regulation and management of wetland ecosystems.