This study investigated the influence of dietary supplementation with Bacillus subtilis natto (BSN) on various physiological parameters in red sea bream (Pagrus major). Key areas of focus included growth performance, enzymatic activity related to digestion, blood biochemical markers, immune function, and intestinal microorganisms. Fish were fed diets containing the following five levels of BSN: 0 (BN0), 1 × 107 (BN1), 1 × 108 (BN2), 1 × 109 (BN3), and 1 × 1010 (BN4) CFU kg−1 for 56 days. Fish in the BN3 and BN4 groups exhibited significantly enhanced growth performance compared to the BN0 group (p < 0.05). Additionally, the activities of amylase and protease were markedly higher in the BN3 and BN4 groups (p < 0.05), while lipase activity was significantly elevated in fish fed the BN3 diet (p < 0.05). Plasma total protein levels also showed a significant increase in the BN3 group (p < 0.05). Hematocrit values were significantly improved in the BN2, BN3, and BN4 groups (p < 0.05). The intestinal microbiota of the BN4 group revealed a significant increase in the populations of B. subtilis and Lactobacillus, along with a notable decrease in Escherichia coli, compared to all other groups (p < 0.05). The observed improvements in specific growth rate and the upregulation of growth-related gene expression further highlight the potential of BSN to enhance the growth performance of red sea bream. In conclusion, dietary supplementation with BSN at 1 × 109 and 1 × 1010 CFU kg−1 shows promise in improving the growth, health, and immune response of red sea bream.