Arenicola cristata represents a classic type of seafood delicacy along the coast of China. The intestinal microbial communities within it play significant roles by engaging in both beneficial and pathological interactions with their hosts. In order to investigate the relationship between the diversity of the intestinal microbiome and the living environment of A. cristata, this research utilized 16S rDNA gene sequencing technology to analyze the microbial population in A. cristatas from shrimp ponds and tidal flats via the PacBio sequencing platform. Moreover, the metabolites of intestinal microorganisms in A. cristatas from shrimp ponds were also detected. The findings demonstrated that the intestinal samples A. cristata from shrimp ponds exhibited a greater number of features, higher richness, and more diverse species when compared to those from tidal flats. Additionally, there was a significant variation in microbial species between the two habitats. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the top annotated metabolites were terpenoids and polyketides, while lipids and lipid-like molecules were most commonly encountered in the Human Metabolome Database (HMDB) database. The LIPID MAPS database indicated that glycerophospholipids (GP) were predominant. The analyses of gut symbiotic microorganisms and the habitat environment furnished evidence on the environmental adaptability of A. cristatas and laid the groundwork for the development of specialized functional strains in the intestinal tract of A. cristatas, as well as for the exploration and utilization of high-quality natural metabolites.