The volatile organic compounds produced by plants and microorganisms have been widely used for postharvest disease control due to their high antifungal capacity. In this research, a volatile product of citrate metabolism, 2,3-butanedione, was assayed against gray mold caused by Botrytis cinerea on postharvest fruit. 2,3-Butanedione treatment exhibited a distinct inhibitory effect on colony growth, conidial germination rate and germ tube length of B. cinerea in vitro and efficiently mitigated the disease prevalence of inoculated fruit under both artificial and natural inoculation conditions. Transcriptome analysis displayed that 2,3-butanedione treatment led to down-regulated expression of genes associated with arginine biosynthesis, ribosome biogenesis and several pathogenicity-related genes, including Bcpg1–3, BcNEP1, Bcboa2 and Bmp1. Furthermore, treatment led to increased genes expression related to proteolysis, peroxisome and autophagy. Among them, the autophagy pathway was most prominent, and key genes in this pathway (BcATGs and BcVPS45) were activated by 2,3-butanedione treatment. Moreover, numerous autophagic vacuoles containing cytoplasmic components were observed in the 2,3-butanedione-treated fungal cells. These results suggest that 2,3-butanedione inhibits gray mold on postharvest fruit by not only interfering the gene expression of fungal growth and pathogenicity in B. cinerea, but also inducing autophagic activity. Collectively, these results provide a theoretical basis for elucidating the underlying antifungal mechanism of 2,3-butanedione against B. cinerea.