Bacterial enteritis is a major disease of bullfrogs that is characterized by rapid onset, high infectivity, and high mortality. This disease causes significant economic losses to the bullfrog farming industry and threatens food and environmental safety. Bacillus coagulans has gained more and more attention in the field of livestock and poultry replacement resistance due to its common advantages of acid-producing bacterial inhibition by Lactobacillus lactis and heat resistance of Bacillus subtilis suitable for feed pelleting. In this study, the therapeutic effect of B. coagulans BC66, administered as a feed supplement, on bacterial enteritis in bullfrogs was revealed based on intestinal flora analysis and serum metabolomics. Bullfrogs with bacterial enteritis were administered B. coagulans BC66 in feed for 20 days, where the concentration of the bacterial solution was 100 billion CFU/g, during which the number of treatments totaled 20, then studies were conducted to analyze intestinal histomorphology, the expression of intestinal proinflammatory factors, microbial diversity of the intestinal mucosa, immune indexes, and metabolite levels in serum. Compared with the untreated group, treatment of bullfrogs with B. coagulans BC66 resulted in repair of the intestinal tissue, a significant reduction in the expression of proinflammatory factors IL-1β, IL-8, IL-17, and TNF-α, increased diversity of microorganisms in the digestive tract, a decreased number of pathogenic bacteria, an increase in the number of probiotics, elevated levels of alkaline phosphatase, lysozyme, lactate dehydrogenase, glycolysin, and creatine kinase, upregulated levels of D-alkaline phosphatase, upregulated D-amino acid metabolism and aminoacyl-tRNA biosynthesis, and downregulated sphingolipid metabolic pathways. These results showed that B. coagulans could effectively treat bacterial enteritis in bullfrogs, increasing their survival rate, enhancing microbial homeostasis of the intestinal tract, reducing the occurrence of inflammation, and enhancing their immune ability. Taken together, the findings of this study provide insight that may aid the management of disease in the bullfrog farming industry, thereby ensuring improved food and environmental safety.