Inulin is a soluble dietary fiber that has been implicated in regulating the intestinal health. Here, we describe a synergetic response of intestinal microbiota and epithelial functions to increased intake of inulin in a porcine model. Twenty growing-pigs were randomly allocated to two groups (n = 10) and fed with a basal diet (BD) or BD containing 0.5% inulin (INU) for 21 days. We show that INU supplementation not only elevated villus height and the abundance of zonula occludens-1 (ZO-1), but also increased acetate and butyrate concentrations in cecum (P < 0.05). Moreover, INU decreased IL-6 and TNFα secretion, and reduced intestinal epithelial cell apoptosis in ileum and cecum (P < 0.05). Interestingly, we observed an elevated 16S rRNA gene copies in cecum after INU ingestion (P < 0.05). INU had no influence on overall diversity, but acutely altered the abundance of specific bacteria. INU decreased the abundance of phylum Proteobacteria in ileum, but increased the phylum Bacteroidetes in the ileum and cecum (P < 0.05). INU significantly elevated the Lactobacillus spp. and Bacteroides spp. in the ileum and cecum, respectively. Importantly, INU elevated the expression levels of GPR43, GLP-2, and ZO-1, but decreased the expression levels of histone deacetylase 1 (HDAC1) and TNFα in the ileum and cecum mucosa (P < 0.05). Moreover, INU also elevated the expression levels of GPR109A and angiopoietin-4 (ANG-4) in the cecum mucosa (P < 0.05). This study indicated how the intestinal microbiome and epithelium adapt to inulin ingestion, and furthered our understanding of the mechanisms behind the dietary fiber-modulated intestinal microbiota and health.