This research was to investigate the efficacy and mechanisms of removal of deoxynivalenol (DON) in wheat flour by Bacillus natto 16-1 by ELISA and high performance liquid chromatography / tandem mass spectrometry (HPLC-MS). The results show that, after 5 hours of culture, the DON removal rates were above 53% in different concentrations of bacterial suspension, fermentation supernatant, bacterial lysis liquid, crude enzyme liquid and cell wall suspension. And there were significant differences among different concentrations of bacterial suspension treatments, and high concentration of cell wall suspension treatment of DON removal rate was up to 62.85%. After 10 hours of culture, the DON removal rate of different bacterial components was above 57%, and there were significant differences among different concentrations of fermentation supernatant, bacterial lysis liquid and cell wall suspension treatment. Except for the cell wall treatment group, all other groups can degrade DON as a small molecule mass substance. The cell components of Bacillus natto 16-1 have a scavenging effect on DON, and this effect is somehow related to the concentration of the cell components and the treatment time. The mechanism of DON removal by each cell component is mainly biodegradation, and the cell wall may removal of DON by biosorption.