Cold plasma (CP) has an inactivating effect on bacteria, but little research has been done on fungi, especially on aflatoxin (AF)-producing strains of Aspergillus flavus (A. flavus). In this study, a CP device was utilized to investigate the destructive effects and mechanisms of different voltage treatments on AF-producing A. flavus strains. The inactivation curve was fitted using Weibull and Logistics kinetic models (R2 > 0.930). The results of viable spore count and AF detection showed that after 6 min of 60 V treatment, the total number of viable spores decreased by 4.47 log10 CFU/mL, and the AF level was found to be significantly lower after treatment (p < 0.05). The microstructure of A. flavus spores was severely damaged after DBDP treatment. The leakage of nucleic acids and proteins, lipid oxidation level, reactive oxygen level, and Fourier transform infrared spectroscopy analysis of spores all confirmed that the cell membrane of A. flavus was damaged after DBDP treatment. This study could provide reference methods for CP technology in the control of AF-producing A. flavus.