Mycotoxin contamination caused by Zearalenone (ZEN) and Ochratoxin A (OTA) is widespread for being prone to happen and hard to degrade. In this paper, the effects of ozone and electron beam irradiation (EBI) on the degradation of Zearalenone and Ochratoxin A were investigated. After 10 s of 2.0 mg/L ozone treatment, the ZEN content decreased from 50 μg/mL to concentration undetectable. After 12 kGy of EBI, the degradation rate of ZEN was up to 86% and concentration of ZEN within 0.5～5.0 μg/mL had no significant different (P＜0.05), with the degradation of ZEN being faster in acetonitrile than methanol. After 30 s of 50 mg/mL ozone treatment, the degradation rate of 5 μg/mL OTA was up to 22%, with no significant improvement of 180 s treatment. After 12 kGy of EBI, the degradation rate of OTA was up to 90% and the concentration of OTA had no significant different (P＜0.05), with the degradation of OTA being faster in acetonitrile than methanol. In general, the degradation of ZEN by ozone was easier than EBI, with EBI being easier than ozone for the degradation of OTA. In this study, a comprehensive study of the application of ozone and EBI on degradation of ZEN and OTA was intended for providing theoretical and practical reference.