Clostridium butyricum (CB) is known to promote growth, enhance immunity, promote digestion, and improve intestinal health. In this study, we investigated the effects of CB in the feed on growth performance, digestion, and intestinal health of juvenile spotted sea bass. To provide a theoretical basis for the development and application of CB in the feed of spotted sea bass, a total of 450 spotted sea bass with an initial body weight of (9.58 ± 0.05) g were randomly divided into six groups. Gradient levels with 0, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% of CB (1×109 cfu/g) were supplemented into diets, designated as CC, CB1, CB2, CB3, CB4, and CB5, respectively. Each group was fed for 54 days. Our results suggest that dietary 0.2% and 0.3% of CB can significantly increase the weight gain (WG) and specific growth rate (SGR) of spotted sea bass. The addition of CB significantly increased intestinal amylase activity, intestinal villus length, intestinal villus width, and intestinal muscle thickness. Similarly, CB supplementation increased the expression of tumor necrosis factor-α (TNF-α) and interleukin-8 (IL-8). Sequence analysis of the bacterial 16S rDNA region showed that dietary CB altered the intestinal microbiota profile of juvenile spotted sea bass, increasing the dominant bacteria in the intestine and decreasing the harmful bacteria. Overall, dietary addition of CB can improve growth performance, enhance intestinal immunity, improve intestinal flora structure, and comprehensively improve the health of spotted sea bass.