Spot disease caused by Alternaria alternata (A. alternata) commonly occurs in postharvest pears, often resulting in severe rot and considerable economic losses. Here, citral, a natural compound, was found to exhibit potential inhibitory effects against A. alternata. The compound could markedly suppress mycelia growth, with a minimum inhibitory concentration of 0.156 g/L, and simultaneously reduce pear fruit decay. Further analysis revealed that citral altered the hyphal morphology of A. alternata and damaged the integrity of cellular membranes, leading to the release of nucleic acids and proteins. In addition, citral treatment was found to inhibit antioxidant enzyme activity, induce the accumulation of reactive oxygen species, and elevated the malondialdehyde level. It also resulted in a dose-dependent reduction in total cellular lipids, proteins, and sugars. Transcriptomic analysis revealed 1658 upregulated and 2741 downregulated genes in the citral treatment group. Among them, genes related to cell membrane lipids, such as those involved in lipid metabolism, glycerolipid metabolism, steroid biosynthesis, and sphingolipid biosynthesis, were notably enriched. Citral also disturbed fungal energy metabolism by affecting glycolysis/gluconeogenesis, the TCA cycle, and galactose metabolism pathways, which was also confirmed by metabolomic analysis. The results suggest that citral can effectively inhibit A. alternata growth by damaging membrane integrity, activating oxidative stress, and disturbing energy metabolism. Our findings provide new insights into understanding citral as a natural antifungal agent for controlling postharvest black spot disease in pears.