Preharvest application of melatonin affected postharvest disease resistance in cherry tomato fruit (Solanum lycopersicum) were conducted after the fruit were sprayed with 0.1 mM melatonin at different growth stages. The results showed that melatonin spray at late stage of enlargement reduced gray mold caused by Botrytis cinerea and natural decay in tomato fruit during storage. Transcriptome analysis identified many differentially expressed genes (DEGs) from tomato fruit upon preharvest melatonin spray, which were mainly associated with calcium signal transduction, salicylic acid (SA) signaling pathway and phenypropanoid metabolism. Preharvest melatonin spray up-regulated expressions of calcium-dependent protein kinase (SlCDPK) and respiratory burst oxidase homologs (SlRBOHs) in relation to radical oxygen species (ROS) burst, and enhanced the contents of SA and lignin and the expressions of most genes involved in SA signaling pathway and phenypropanoid metabolism, which were contributed to enhancing disease resistance of cherry tomato fruit during storage.