Gut microbiota have been linked to atherosclerosis (AS). This study aimed to investigate the differences in gut microbiota between patients with AS and healthy controls using third-generation gene sequencing.Full-length 16S rRNA amplicon sequencing was used to compare the composition, abundance, diversity, and differences in intestinal flora between a healthy control group (ASC, N.=20) and an atherosclerotic patient group (ASP, N.=21).The ASP group showed higher rank richness and an altered microbial community structure compared to the control group. We found 12 phyla and 201 bacterial taxa in our samples, with Firmicutes being the most abundant phylum in both groups. However, several bacterial species, including Lactobacillus fermentum, Escherichia coli, Dialister succinatiphilus, and Fusobacterium varium, were more abundant in the ASP group. Except for Escherichia coli, the other three bacterial species are associated with lipid metabolism. The ASP group exhibited smaller network diameters, lower graph density, and lower average degree than the ASC group, indicating greater correlations and clustering of operational taxonomic units samples. Functional profiling showed significant enrichment in AMPK signaling pathway and glucose metabolism in the ASC group, while bacterial invasion of epithelial cells was enriched in the ASP group.Our findings aid in enhancing the comprehension of the gut microbiota's role in AS development and provide valuable insights for potential therapeutic interventions.