The present study aimed to investigate the effect of Bacillus subtilis (B. subtilis) on the residue, metabolism, and biotransformation of deoxynivalenol (DON) in broiler chickens. There were 7 dietary treatments including a control and a factorial design with two factors, DON at 3 and 6 mg/kg and B. subtilis at 0, 106 and 109 CFU/kg of diet. A total of 420 broiler chickens at one day old were randomly distributed to 7 groups with 6 replicates of 10 chickens each. The feeding trial lasted for 21 days. Results showed that DON decreased and B. subtilis increased feed intake, body weight gain, and feed efficiency; and an interaction was found on feed intake. In the liver and ileal digesta, the two dietary factors conversely influenced the contents of DON residue and the metabolites (DON glucuronides and deepoxy-deoxynivalenol) of enzymes and microbe; and there was an interaction on deepoxy-deoxynivalenol. Also, in the liver and ileal mucosa, the activities of detoxifying enzymes (cytochrome P450, glutathione s-transferase α, epoxide hydrolase 1, and uridine diphosphate glucuronosyltransferase) and inflammatory factors (interleukin 1β, tumor necrosis factor α, interleukin 6, and interleukin-1 receptor antagonist) were conversely changed by the two dietary factors; and there were interactions on epoxide hydrolase 1, interleukin 1β, and tumor necrosis factor α. Additionally, B. subtilis at 109 CFU/kg showed greater effects on deepoxy-deoxynivalenol, epoxide hydrolase 1, and tumor necrosis factor α than that of 106 CFU/kg. It is concluded that the selected probiotics can decrease DON toxicity by microbial transformation and enzymatic metabolism in farm animals.