Abstract: As key benthic organisms in coastal intertidal ecosystems, crabs harbor gut microbiota play critical roles in host environmental adaptation. To explore how intertidal habitats heterogeneity influences the structure and function of crab gut microbiota in the Yellow River Delta, this study analyzed the diversity, compositions, interaction networks and potential functions of crab gut bacterial communities in low (LM), middle (MM), and high (HM) tidal marshes using 16S rRNA high-throughput sequencing. The results showed that: (1) The diversity of crab gut bacterial community varied among the three marshes, with the highest species diversity (Shannon index) in HM and the highest species richness (Chao1 index) in LM. (2) The compositions and abundances of predominant bacteria were distinctly different across tidal marshes. LEfSe analysis showed that Proteobacteria (42.70%) and Actinobacteriota (12.21%) were the biomarker taxa in HM, while Firmicutes (57.64%), Bacteroidota (13.28%), and Desulfobacterota (4.23%) were the biomarker taxa in LM, respectively. (3) The topologies of the co-occurrence networks differed markedly. Specifically, the HM network exhibited lower connectivity and weaker clustering with reduced average degree (2.43), graph density (0.028), modularity (0.22), and fewer key nodes (10 OTUs) compared to those in MM and LM. (4) PICRUSt2 prediction indicated that bacterial community functions in HM differed from those in MM and LM, with significantly higher relative abundances of carbon and nitrogen metabolism, membrane transport, and signal transduction. In conclusion, this study revealed that intertidal habitat heterogeneity significantly affected the community structure, interaction network, and metabolic function of crab gut microbiota, providing a theoretical basis for analyzing the ecological adaptability mechanisms of macrobenthos in the Yellow River Delta wetland.