The study examined gut microbiota and metabolic profiles in 432 patients after gallbladder removal (cholecystectomy), comparing those with metabolic syndrome and without. Patients with metabolic syndrome showed reduced microbial richness and a lower Firmicutes/Bacteroidetes ratio, with higher Prevotella abundance and lower levels of Bacteroides, Faecalibacterium, and Roseburia. Metabolomic analysis revealed elevated secondary bile acids and decreased short-chain fatty acids, particularly butyrate. These changes were associated with inflammatory markers and adverse metabolic indicators. The results indicate that post-cholecystectomy patients with metabolic syndrome have distinct microbial and metabolomic profiles compared to patients without metabolic syndrome.