Electron beam irradiation is a physical fungicidal technique that has emerged as a potential application in China. However, its antifungal activity and mechanism against Rhizopus oryzae have not been reported. Thus, this study aimed to investigate the antifungal activity and mechanism of electron beam irradiation of R. oryzae. The antifungal activity analysis showed that the D10 value and complete elimination dose of R. oryzae irradiated by electron beam were 1.73 kGy and 8.08 kGy, respectively. Electron beam irradiation has a strong inhibitory effect on the filamentous biomass of R. oryzae. To reveal the antifungal mechanism of electron beam against R. oryzae, this study analyzed the dynamic changes in the cell wall, cell membrane, and oxidative stress induced by different irradiation doses. The results showed that electron beam irradiation destroyed the cell wall structure of R. oryzae, increasing chitinase activity and decreasing chitin content. Cell membrane integrity is disrupted, increasing relative conductivity, decreasing pH values, and decreasing soluble protein content. Electron beam irradiation causes oxidative stress in cells, increasing H2O2 content, decreasing antisuperoxide anion activity, decreasing DPPH free radical scavenging activity, and inhibiting defense enzyme (CAT and SOD) activity. This phenomenon indicates that electron beams can cause structural damage to and metabolic dysfunction of cells and disorders of redox homeostasis, which may be the main cause of growth inhibition and cell death in R. oryzae.