This study evaluated the effects of dietary Clostridium butyricum on intestinal enzyme activity, intestinal histology, immune-related gene expression, short-chain fatty acids and intestinal microbiota in common carp (Cyprinus carpio L.). Three hundred and sixty fish (89.89 ± 0.77 g) were divided into three groups and fed a diet supplemented with C. butyricum at 0, 0.125% (0.25 × 107 CFU/g), or 0.5% (1 × 107 CFU/g) (denoted as NC, LCB and HCB, respectively) for 8 weeks. Compared with the NC group, growth performances were not affected by adding C. butyricum. The enzyme activity of catalase (CAT) and lysozyme (LZM) in the intestine of the HCB group were significantly enhanced, and the butyric acid and propionic acid content in both C. butyricum-treated groups increased. In the HCB group, mucin secretion and the height of the epithelium microvilli were obviously increased, and the mucosal folds were deeper and smoother. The intestinal gene expression of IL-10, TLR-2, MyD-88, ZO-1 and Occludin were significantly higher in the HCB group than that in the control group but not in the LCB group. Dietary C. butyricum increased the diversity of the intestinal microbiota of common carp. At the phylum level, the abundance of Bacteroidetes improved concomitantly with a significant decrease in the abundance of Fusobacteria and Proteobacteria. At the genus level, the relative abundance of the beneficial bacteria Bacteroides and Cetobacterium increased remarkably in the HCB group, and pathogens such as Aeromonas, Vibrio, and Pseudomonas were inhibited. In conclusion, the results from this study indicate that supplementing the diet with C. butyricum at an appropriate dose can improve the intestinal immunity of common carp by regulating the intestinal microbiota and improving the defence function of the intestinal barrier.