The present study investigated the growth performance, immune status, gut morphology, and gut microflora modulation in growing-to-finishing pigs (n = 72; 24 pigs/group) after dietary supplementation with Bacillus subtilis (B. subtilis; two groups (experiment 1 (E1) and experiment 2 (E2): 63 and 98 days, respectively) and control (Ct, basal diet). The results revealed that both 1–98 d and 1–63 d groups significantly improved growth performance, including an increase in midtest body weight (MBW) P = 0.0114 , final body weight (FBW) P < 0.0001 , and average daily gain (ADG) P < 0.0001 and a decrease in the ratio of feed to gain (F/G) P < 0.0001 . There was an increase in serum IgG and SOD levels after supplementation with B. subtilis P = 0.0074 . Furthermore, B. subtilis potentiated the integrity of intestinal morphology (villus height (VH) P < 0.0001 and villus height/crypt depth (VH/CD) P = 0.0009 ) in growing-to-finishing pigs. The LEfSe analysis identified 11 and 13 biomarkers in the fecal samples of the 1–63 d group and 1–98 d, respectively. The gut microflora alterations of growth-finishing pigs suggested that dietary B. subtilis could promote gut health by altering the relative abundances of different bacterial communities. A correlation analysis showed that B. subtilis could regulate the functional network of the intestine microflora and their interactions with its host. Taken together, dietary B. subtilis supplementation had a positive influence on the growth performance, gut health, and the composition of gut microorganisms, suggesting that B. subtilis can be used as a functional probiotic candidate for application in the production of growing-to-finishing pigs. Practical Applications. The addition of probiotics in the diet can modulate intestinal health, improve the digestibility of nutrients, and thus, help improve the nutrient utilization and production performance of pigs. It is one of the ideal substitutes for antibiotics. This study will help us understand the function of B. subtilis in the regulation of pig intestinal health, so as to provide scientific basis for the rational use of probiotics in the future pig industry.