Reducing the postharvest loss of cereal grains caused by deleterious fungi is critically important for the grain supply chain. Exploring antifungal constituents of plant volatile organic compounds (PVOCs) could promote the development of natural gaseous fungicides in controlling the decay of postharvest grains. In this study, PVOCs were extracted from clove ( Syzygium aromaticum L.) buds and the primary constituents thereof were investigated for their effect on Aspergillus flavus growth in media postharvest grains. Fumigation with clove buds’ volatiles effectively inhibited A. flavus proliferation in 20% moisture wheat grains under simulated storage conditions. Gas chromatography-mass spectrometry analysis revealed that eugenol and caryophyllene were the two main constituents of clove bud volatiles (49.80% and 36.68%, respectively). An antifungal assay demonstrated that eugenol was responsible for the antifungal activity of clove bud volatiles against A. flavus. Eugenol can completely inhibit A. flavus growth at 0.12 and 0.40 μL/mL in vapor phase fumigation and liquid contact, respectively. The proliferation of A. flavus in 20% moisture wheat grains was completely controlled after fumigation with 600 μL/L eugenol vapor. Eugenol treatment can damage the membrane integrity of A. flavus mycelia, resulting in increased intracellular electrolyte leakage. The 38 metabolites in A. flavus hyphae exposed to 0.40 μL/mL eugenol were markedly differentially expressed and principally involved in the biosynthesis of glycerophospholipids, linoleic acid metabolism, fatty acid metabolism, sugar metabolism, and ATP-binding cassette transporters. Eugenol also causes phosphatidylserine eversion of the plasma membrane, increased reactive oxygen species, decreased ATP production, and damaged DNA in A. flavus . We propose that eugenol treatment can disrupt cell membrane integrity, fatty acid β -oxidation, and induce apoptosis in A. flavus . This study demonstrated the potential application of clove bud volatile organic compounds as biofumigants for postharvest grain management and provided new insights into the antifungal mechanism of the main constituents against A. flavus growth. • Clove volatiles from Syzygium aromaticum , L. could control Aspergillus flavus growth in wheat grains. • Eugenol and caryophyllene are the two main volatile components of clove determined by GC-MS. • Eugenol could inhibit the growth of A. flavus in vapor phase and liquid contact. • The antifungal actions of eugenol on A. flavus were studied by metabolomic and biochemical analyses. • Eugenol could be used as biofumigants for postharvest grain management.