The inhibitory effects of ClO2, clove essential oil and cinnamon essential oil on Fusarium graminearum were studied by observing the colony diameter, mycelial growth and spore germination. The results showed that ClO2, clove essential oil and cinnamon essential oil had significant inhibitory effect on Fusarium graminearum, among which, clove essential oil had lower inhibitory effect than cinnamon essential at low density (20~40 µL/L air), and its inhibitory effect was improved dramatically and better than cinnamon essential with the increase of density. Through the regression equation of inhibition rate, the IC50 of ClO2, clove essential oil and cinnamon essential oil were 27 mg/L, 58 µL/L air and 66 µL/L air respectively. By means of ergosterol content determination, scanning electron microscope observation and Fourier transform infrared analysis, we found that ClO2 and essential oil destroyed cell structure in different degrees, ClO2 destroyed cell membrane, leading to the exudation of contents. High density of clove essential oil destroyed cell structure, while cinnamon essential oil resulted in maldevelopment of mycelium.