Probiotics are thought to have immunomodulatory functions, improve inflammatory disorders and treat inflammatory bowel disease (IBD). Here, we screened a new probiotic strain with anti-inflammatory activity and investigated its effect on the immune cell response and histone acetylation. Lactobacillus casei (L. casei) LH23 inhibited the production of nitric oxide and inflammatory factors induced by lipopolysaccharides in RAW264.7 cells, which was associated with inhibiting the over-activation of the JNK/p38 signaling pathway. Furthermore, L. casei LH23 can significantly ameliorate dextran sulfate sodium (DSS)-induced mouse colitis in vivo by reducing numbers of macrophages (CD11b+F4/80+) and their secreted inflammatory cytokines. Myeloperoxidase activity was also decreased in mice treated with LH23. The administration of L. casei LH23 induced the increase of CD3+CD4+CD25+ regulatory T cells among mesenteric lymph nodes. Meanwhile, LH23 treatment could augment short chain fatty acid contents. Importantly, we reported here for the first time that DSS treatment significantly decreased the level of histone H3K9 acetylation, while supplementation of L. casei LH23 restored the level of histone H3K9 acetylation in colon tissues. These data suggest that L. casei LH23 may have been beneficial for preventing and treating IBD.