Abstract: In order to understand the intestinal microbial community structure and metabolome characteristics of the Dinghai bay Capitulum mitella, explore the relationship between the living environment, feeding habits and gut microbiota composition of the Capitulum mitella, this paper used 16S rRNA high-throughput sequencing technology and non targeted metabolomics techniques to analyze the Capitulum mitella samples collected. The results showed that at the phylum level, the most dominant phylum in the gut microbiota of the Capitulum mitella is Proteobacteria, with a content of 47.17%, followed by Bacteroidota with 40.61% content. At the class level, the most dominant class was Bacteroidia(40.59%), followed by Gammaproteobacteri(32.62%). In terms of genus, the most dominant genus is Sediminibacterium with a content of 22.77%, followed by Pseudarcicella with a content of 10.97%. There are still more genera that can't be cultured or identified. At the same time, non-targeted metabolome analysis was carried out on the intestinal samples of Capitulum mitella. The results showed that lipid and lipids accounted for 31% of the total metabolites in the intestinal metabolites, followed by organic acids and their derivatives, accounting for 23% of the total metabolites.