Inulin has been reported to alleviate colitis. In this study, colitis patients' feces were used to simulate fermentation to demonstrate changes in the microbiota profile in the presence of inulin. We found inulin can reshape the gut microbiota profile of colitis patients, especially by altering the abundance of Faecalibacterium and Blautia. Interestingly, the subsequent co-culture with inulin demonstrated that inulin promoted the growth of these two strains of bacteria. The dextran sodium sulfate (DSS)-induced mouse model was used to examine the effect of inulin and its combination with two probiotics on colitis. Results showed that all three treatments can alleviate the clinical symptoms, including weight-losing, colon-shortening, and the Disease Activity Index (DAI) score. Further investigations showed that the administrations regulate colitis mice's pro- and anti-inflammatory cytokines, such as TNF-α, IL-1β, IL-6, IL-10, and IL-17. Also, they alter the relative abundance of Faecalibacterium and Blautia, change the short-chain fatty acids (SCFAs) profile in the cecum and colon, and improve the intestinal barrier; specifically, the intervention increased the expressions of Claudin, Occludin, Zonula Occludens (ZO)-1, and Mucin (MUC)-2 in colonic tissues, thus restoring the colonic tissue structure and morphology of colitis mice. Collectively, our results confirm that inulin can alter the colitis patients' characteristic microbial community, and they can ameliorate experimental colitis by inhibiting the TRL4/MyD88/NF-κB signaling pathway—improving the inflammatory response and enhancing the intestinal barrier. In conclusion, we propose that inulin may hold promise as a functional food therapeutic approach for the treatment of colitis.