Non-digestible oligosaccharides have attracted attention due to their critical role in maintaining the balance of a host's gut microbiota. Lactiplantibacillus plantarum ZDY2013 was isolated from traditional fermented acid beans, which could metabolize many complex carbohydrates and had intestinal immunomodulatory effects. In our study, the ameliorative effect of a combination of non-digestible isomaltooligosaccharide (IMO) and L. plantarum ZDY2013 was investigated in dextran sulfate sodium (DSS)-induced colitis mice. The results showed that IMO could specifically promote L. plantarum ZDY2013 intestinal colonization after five days of gavage and ameliorate the symptoms of colitis (survival rate, DAI score, colon length, etc.) as well as colon tissue integrity. IMO combined with L. plantarum ZDY2013 increased the levels of intestinal tight junction proteins (ZO-1 and claudin) and mucin (MUC-2), followed by alleviation of inflammatory responses (decreased the expression of IL-1β, TNF-α, and IL-6 and increased the expression of IL-10 and IL-22) and the level of oxidative stress (decreased the level of COX-2 and iNOS and increased the expression of T-AOC and SOD). Furthermore, the combination increased the diversity of the gut microbiota and modulated the microbial structural component (decreased the abundance of Escherichia and Helicobacter and increased the abundance of Lactobacillus and SCFA-producing related species). Taken together, our results suggested that the consumption of IMO and L. plantarum ZDY2013 could improve the symptoms of colitis in mice by improving the intestinal barrier along with regulating the composition and metabolites of the gut microbiota.