This study investigated the effects of inulin on mucosal morphology and immune function of specific pathogen-free (SPF) chickens. A total of 200 one-day-old White Leghorns SPF chickens were divided into 5 groups of 4 replicates of 10 chickens each. All SPF chickens were fed a basal diet supplemented with 0, 0.25, 0.5, 1.0, or 2.0% inulin. The mucosal morphology and immune indexes were analyzed on days 7, 14, and 21, respectively. Our results showed that the concentrations of acetate and propionate in the cecum and serum had increased with dietary inulin supplementation on day 21 (P < 0.05). Butyrate could not be detected in the cecal digesta, but was increased in the serum of 1 and 2% groups, as compared with the control group (P < 0.05). The villi height was increased (P < 0.05) and the crypt depth was decreased (P < 0.05) in the duodenum and ileum of SPF chickens fed inulin, as compared with the control group. Also, inulin at a low concentration (0.25 or 0.5%) significantly decreased (P < 0.05) the gene expression of nuclear factor-κB (NF-κB), lipopolysaccharide-induced tumor necrosis factor (LITAF) at 7, 14, and 21 d, and of interleukin-6 (IL-6), and inducible nitric oxide synthase (iNOS) at 7 and 14 d, and increased that of mucin 2 (MUC2) and claudin-1 in the ileum of SPF chickens at 7, 14, and 21 d. High inulin supplementation (2%) significantly increased the gene expression of NF-κB, LITAF, IL-6, iNOS, and Claudin-1 at 14 and 21 d compared to low inulin concentration (0.25 or 0.5%). The results indicated that the effects of inulin on mucosal immune function occurred in a dose-dependent manner. A low concentration (0.25 or 0.5%) of inulin may be beneficial in promoting intestinal immune function.