Objective: To explore the structural characteristics of intestinal microbiota in patients with sepsis-associated acute kidney injury (SA-AKI) and analyze its correlation with clinical severity and inflammatory response indicators, so as to provide evidence for elucidating the pathogenesis of SA-AKI and identifying novel therapeutic targets. Methods: A total of 45 patients with SA-AKI were selected as the case group, and 30 healthy individuals were included as the control group. Fecal samples were collected to analyze the α-diversity and β-diversity of the intestinal microbiota as well as the microbial composition. The correlation between the microbiota and clinical indicators was also evaluated. Results: Compared with the control group, the α-diversity (Shannon index and Chao index) of the intestinal microbiota in the casegroup was significantly reduced (P<0.05). The abundance of Proteobacteria was significantly increased in patients of the case group, while the proportions of Firmicutes and Bacteroidetes were markedly decreased. Correlation analysis revealed that the abundance of Enterococcus was significantly positively correlated with both the Sequential Organ Failure Assessment (SOFA) score and serum creatinine levels, whereas the abundance of Faecalibacterium was significantly negatively correlated with interleukin-6 levels. Conclusion: Significant intestinal dysbiosis is present in patients with SA-AKI, characterized by reduced microbial diversity, altered microbial structure, and overgrowth of opportunistic pathogens. This dysbiosis is closely associated with the severity of the disease and systemic inflammatory response. These microbial taxa hold promise as potential biomarkers and therapeutic targets.