Fusarium is a kind plant pathogenic fungus, resulting in severe crops infection and food safety issues. The development of novel strategy to inactive Fusarium is in urgent need. In this study, the inactivation effect and mechanism of dielectric barrier discharge (DBD) plasma on Fusarium verticillioides was studied. The results showed that the fungicidal effect of DBD plasma was positively correlated with the voltage strength and treatment time, which could reach 100% sterilizing rate at 60–80 V. The scanning electron microscope (SEM) observation indicated the integrity of the cell wall and cell membrane of the treated F. verticilliordes was damaged, leading to leakage of the contents. The changes of mitochondrial membrane potential, adenosine 5′-triphosphate (ATP) content, cell viability and reactive substances (intracellular reactive oxygen species (ROS), intracellular hydrogen peroxide (H2O2), ozone (O3) and reactive nitrogen species (RNS) (NO2−, NO3−, etc.)) were also tested to better understand the fungicidal mechanism of cold plasma. These results demonstrated DBD plasma could be a promising technique for Fusarium inactivation in food.