The pathogenesis of inflammatory bowel disease (IBD) might be related to the local inflammatory damage and the dysbacteriosis of intestinal flora. Probiotics can regulate the intestinal flora and ameliorate IBD. The probiotic strain JNFE0126 was used as the starter of fermented milk. However, the therapeutic effects of -fermented milk on IBD remain to be explored. In this research, the therapeutic effect of fermented milk on dextran sulfate sodium salt (DSS)-induced IBD mouse model was evaluated. Besides, the expression of pro-inflammatory/anti-inflammatory cytokines, the proliferation of the intestinal stem cells, and the reconstruction of the mucosa barrier were investigated. Finally, alteration of the gut microbiota was investigated by taxonomic analysis. As shown by the results, the disease activity index (DAI) of IBD was significantly decreased through oral administration of (JNFE0126)-fermented milk, and intestinal mucosa injury was attenuated. Moreover, could reduce the inflammatory response of the intestinal mucosa, induce proliferation of the intestinal stem cell, and promote reconstruction of the mucosal barrier. Furthermore, could rebalance the intestinal flora, increasing the abundance of , , and while decreasing the abundance of and . In conclusion, oral administration of the -fermented milk could alleviate DSS-induced IBD inhibition of inflammatory response, promotion of the mucosal barrier reconstruction, and regulation of the intestinal flora.