Objective To investigate the structural and diversity characteristics of the gut microbiota in sepsis patients using 16S rRNA gene sequencing technology, and to preliminarily explore their associations with in-hospital prognosis. Methods A prospective study was conducted to collect fecal samples within 2 days of admission from 50 sepsis patients (sepsis group), while fecal samples from 10 healthy volunteers (healthy group) were collected randomly. The V3-V4 region of the fecal bacterial 16S rRNA gene was sequenced, followed by bioinformatics analysis (including operational taxonomic unit, α-diversity, β-diversity, and species composition analyses). Based on in-hospital outcomes, sepsis patients were divided into a survival group (n=40) or a death group (n=10). Bacterial genus proportions between the two groups were compared, and receiver operating characteristic (ROC) curve analysis was used to evaluate the association between the bacterial genus proportions and prognosis. Results The α-diversity analysis showed that the sepsis group had significantly lower Shannon and Simpson diversity indices compared to the healthy group (all P<0.05). The β-diversity analysis indicated structural differences in microbiota between the two groups. In terms of species composition, the relative abundance of Firmicutes was lower in the sepsis group, while that of Proteobacteria was higher. At the genus level, Enterococcus, Bacteroides, and Lactobacillus were the dominant genera in the sepsis group. Prognostic analysis revealed that the death group had a higher proportion of Enterobacter compared to the survival group (P<0.05), and the area under the ROC curve for its association with mortality was 0.744. Conclusions Sepsis patients exhibit gut microbiota dysbiosis, characterized by reduced diversity, decreased beneficial bacteria, and increased opportunistic pathogens. This study preliminarily suggests an association between the relative abundance of Enterobacter and patient mortality. However, its value as an independent prognostic marker requires further validation in large-scale prospective studies with control for key clinical confounding factors.