Piglet diarrhea is a major problem in industrial swine production, causing significant economic losses. This study investigated the efficacy of a *Bacillus*-based probiotic formula (*Bacillus subtilis* Y-15, *B. amyloliquefaciens* DN6502, and *B. licheniformis* SDZD02) in treating piglet diarrhea and restoring the gut microbiome. Illumina sequencing of fecal DNA revealed that the probiotic treatment effectively cured diarrhea and re-established a healthy gut microbiota, unlike antibiotic treatment which negatively impacted the gut flora. The findings suggest a promising natural alternative for treating piglet diarrhea in industrial settings.