Although postharvest partial dehydration has been applied to enhance blueberry wine flavor by increasing terpene level, berry decay remains a concern. Melatonin is known to improve fruit resistance during storage, but its role in terpene accumulation in blueberries during postharvest dehydration remains unclear. This study identified aroma-active terpenes of blueberry wines applying aroma extract dilution analysis and revealed the key genes linked to the increased terpenes in dehydrated blueberries. Further investigations studied the effects of melatonin on key terpene accumulation in dehydrated blueberries. Results showed that melatonin (250 μmol/L) reduced berry decay and increased total terpene content by five folds compared to undehydrated blueberries. Besides, melatonin could interact with ethylene, mitigating the inhibitory effects of 1-methylcyclopropene (1 μL/L) on terpene accumulation. The increased terpene by melatonin could be associated with upregulated VcDXS, VcHDR and VcTPS genes, particularly VcTPS was characterized as a monoterpene synthase, mainly producing linalool.