Probiotics have been shown to inhibit the development of IBD but the specific mechanism remains unclear. In this study, the mitigating effect and underlying mechanisms induced by Lactobacillus plantarum ZJUIDS04 (L. plantarum ZJUIDS04) on dextran sulfate sodium (DSS)-induced colitis in C57BL/6 mice were investigated. After L. plantarum ZJUIDS04 feeding, symptoms of DSS-induced colitis were remarkably reduced, including weight loss, colon shortening, colonic tissue damage, decreased tight junction protein, and pro-inflammatory cytokines. Furthermore, L. plantarum ZJUIDS04 significantly altered the structure of the intestinal microbiota, including decreasing the abundance of Romboutsia, Escherichia − Shigella, and Parabacteroides, as well as increasing the abundance of Akkermansia and Ruminococcus_1. More importantly, the genera of butyric acid-producing bacteria as well as short-chain fatty acids (SCFAs) were increased after L. plantarum ZJUIDS04 intervention, indicating regulation of gut microbiota and its metabolism might be an important factor for L. plantarum ZJUIDS04 alleviation against colitis.