Melatonin (MT) has been reported to alleviate chilling injury (CI) in postharvest tomato fruit during low-temperature storage. In the present study, the DNA methylation profile changes in the CpG islands of ethylene signaling genes regulated by MT in postharvest tomato fruit during low-temperature storage were detected. The MT treatment increased the content of total soluble solids (TSS) and enhanced the ethylene production of tomato fruit. Moreover, it decreased titratable acidity (TA) content, inhibited the activity of polygalacturonase (PG), and kept the firmness of tomato fruit under low-temperature storage. In the MT-treated tomato fruit, significant changes in DNA methylation of CpG island of SlACS10, LeCTR1, LeEIN3, SlERF-A1, and LeERT10 genes were induced; the expression of LeCTR1 was inhibited; and the expression of SlACS10, LeEIN3, and SlERF-A1 genes was increased, by which the ethylene signaling might be influenced and the CI was alleviated. The present results provide evidence that the CI of postharvest tomato fruit alleviated by MT might be related to the changes in DNA methylation of ethylene-signaling genes.