Abstract: As one of the main oil-bearing crops in China, peanuts are susceptible to the contamination of Aspergillus flavus during processing and storage, which results in the loss of commercial values. Hence, it is crucial to investigate the signaling molecules during the early stage of contamination in order to monitor and control the spread of A. flavus in peanuts. In this study, Gas chromatography–ion mobility spectrometry (GC-IMS) was used to analyze the volatile organic compounds (VOCs) during the invasion of A. flavus in peanuts. A total of 53 compounds were detected, including 34 confirmed monomers and dimers. The other 19 compounds were yet to be qualitatively determined. The results showed that the organic compounds produced by A. flavus varied significantly in the different growth stages. The fingerprint spectrum demonstrated the changing patterns and relative concentrations of the volatile organic compounds as the contamination progressed, and the characteristic peaks could be used to quantify the level of contamination at the early stages. The volatile organic compounds were also analyzed with heat map clustering and principal component analysis. Significant differences were observed among the volatile organic compounds at different stages of contamination. The study determined that caproic acid, 2, 3-butanedione, 2-hexen-1-ol-M, pentan-1-ol-M and hexanal could be used as the signaling molecules during the early stages of A. flavus contamination. The results of this study provide an effective marker for the development of early warning monitoring system for peanut mildew degree under storage conditions.