The effect of Rho18 treated with different methods on the removal of deoxynivalenol (DON) from wheat flour was determined by ELISA and HPLC-MS. Processing results showed that the different ways of rice root mildew Rho18 clearance to DON in wheat flour were all increased with the concentration increase with the extension of incubation time, as well as the high concentration of the treatment group. After 10 h incubation with the rest of the concentration of treatment group were significantly different, the cell walls of a high concentration of suspension and wheat 10 h incubation conditions to DON removal effect is best (51.62%). Three kinds of new substances with relative molecular weight of 277, 279 and 281 were produced by Rho18 and DON treated in different ways. The results showed that Rho18 of Rhizopus oryzae treated in different ways had certain scavenging effects on DON, and the effect was related to concentration and incubation time, and its scavenging mechanism was mainly the action of biological enzyme system.