The harm of Aspergillus flavus (A. flavus) and aflatoxin is a severe food safety problem worldwide, which causes huge economic losses every year. Therefore, it is urgent to control the growth of A. flavus and the biosynthesis of aflatoxin. Plant-derived natural compounds are superior to synthetic fungicide in inhibiting the growth of A. flavus benefiting from their high safety to the environment, humans and stock, and low cost. This study aimed to evaluate the antifungal effects and potential antifungal mechanisms of three plant-derived compounds (octanal, nonanal and decanal) against A. flavus. We determined the minimum inhibitory concentrations (MICs) and action mechanism of the three volatile aldehydes on A. flavus and also performed calcofluor white (CW) staining for visualizing the distribution of septa. Cell respiration metabolism and the pathogenicity on maize kernels were also carried out to evaluate the efficacy of the three volatile aldehydes on the growth of A. flavus. The results showed that the three volatile aldehydes could inhibit the germination of spores and mycelial growth of A. flavus, the MICs on spores and mycelia were: octanal (1.0 and 0.5 μL/mL), nonanal (0.5 and 2.0 μL/mL), and decanal (1 and 5 μL/mL). The three volatile aldehydes could strongly damage the integrity of both the cell wall and the cell membrane of A. flavus. Meanwhile, they could decrease the content of total lipid and inhibit respiration metabolism of A. flavus cell. Results of in vitro antifungal test showed that all the three volatile aldehydes could effectively prevent the growth of A. flavus on maize kernels. The study revealed that octanal, nonanal and decanal could effectively inhibit the growth of A. flavus both in culture medium and on maize kernels to different extent. The results confirmed that the plant-derived compounds could be developed into promising antifungal agents applied in the preservation of grains. This study provides a theoretical basis for the research and application of potential antifungal agents.