The gut microbiota, which plays a vital role in synthesizing short-chain fatty acids (SCFAs), is involved in the pathogenesis of inflammatory bowel disease (IBD). This study aimed to evaluate four phyla of gut microbiota and main SCFAs in IBD patients compared to the control group. Stool samples from 40 IBD patients [including ulcerative colitis (UC) and Crohn's disease (CD)] and 20 healthy controls were analyzed. Quantitative polymerase chain reaction was used to assess the abundance of four major gut microbiota phyla, and SCFA concentrations were measured using high-performance liquid chromatography. Results showed that Firmicutes levels were significantly lower in both UC and CD patients compared to controls. Bacteroidetes were significantly reduced in CD patients, while proteobacteria were significantly elevated in UC patients. No significant differences were observed in Actinobacteria levels. Regarding SCFAs, butyric acid was significantly lower in both UC and CD patients. Additionally, acetic acid and propionic acid were significantly decreased only in UC patients. These findings highlight the presence of gut dysbiosis and altered SCFA profiles in IBD patients. Given the protective roles of gut microbiota and their metabolites, strategies to restore microbial balance and SCFA production may support the management and treatment of IBD.