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<i>Bacillus licheniformis</i> (<i>B. Licheniformis</i>) has been considered to be an effective probiotic to maintain gut health and boost productivity in the pig industry, but there is no complete understanding of its mechanisms. We determined whether weaned piglets exposed to <i>BL</i>−S6 (probiotic) had altered intestinal barrier function or microbiota composition. In our study, 108 weaned piglets (54 barrows and 54 gilts) were divided equally into three groups, each with six pens and six piglets/pen, and fed a basal diet supplemented without or with antibiotic (40 g/t of Virginiamycin and 500 g/t of Chlortetracycline) or probiotic (1000 g/t of <i>B. Licheniformis</i>) for a 14-day trial. On day 14, one piglet was chosen from each pen to collect blood and intestinal samples. Compared with the control group, dietary supplementation with a probiotic promoted body weight (BW) gain and average daily gains (ADG) while reducing diarrhea incidence (<i>p</i> < 0.05). Probiotics enhanced superoxidase dismutase (SOD) activity and decreased malondialdehyde (MDA) levels in serum (<i>p</i> < 0.05), and increased the level of mRNA expression of <i>SOD1</i>, <i>Nrf2,</i> and <i>HO-1</i> (<i>p</i> < 0.05) in the jejunum mucosa. Moreover, supplementation with probiotics improved intestinal mucosal integrity as evidenced by higher villus heights and a higher ratio of villus heights to crypt depths (duodenum and jejunum) and higher mRNA and protein levels of occludin and ZO-1 in jejunum mucosa (<i>p</i> < 0.05). The intestinal sIgA levels (<i>p</i> < 0.05) were elevated in the probiotic group, and that of serum immunoglobulin A (IgA) tended to be higher (<i>p</i> = 0.09). Furthermore, weaning piglets who were given probiotics had a better balance of the cecum microbiota, with <i>lactobacillus</i> abundance increased and <i>clostridium_sensu_stricto_1</i> abundance decreased. In conclusion, dietary supplementation with the probiotic <i>BL</i>−S6 promoted intestinal integrity, which was associated, in part, with modulating intestinal barrier function and microbial diversity in weaned piglets; it may offer a promising alternative to antibiotics to prevent diarrhea.