Electron beam irradiation (EBI) has high energy, no induced radioactivity, and strong degradation capacity toward mycotoxins, such as zearalenone (ZEN) and ochratoxin A (OTA). In this study, we determined EBI's influence on the physical and chemical properties of corn contaminated with ZEN and OTA. Moreover, the toxicity of corn after EBI was assessed through a mouse experiment. Amylose content and starch crystallinity in corn decreased significantly ( < 0.05) at an irradiation dose higher than 20 kGy. Scanning electron microscopy results revealed that the starch particles of corn began to be crushed at 10 kGy. Essential and total amino acid contents in corn decreased significantly with increasing irradiation dose of EBI ( < 0.05). Feeding EBI-treated corn fodders to mice could significantly improve blood biochemical indexes. The EBI-treated group was not significantly different from the normal corn group and did not display histopathological changes of the liver. EBI treatment can influence the quality of corn to some extent and effectively lower the toxicity of ZEN and OTA in contaminated corn. The results provide a theoretical and practical basis for the processing of EBI-treated corn and its safety.