Methyl jasmonate (MeJA) has shown promising applications in mitigating fruit quality deterioration. However, whether pre-harvest spraying of MeJA enhances post-harvest grape antioxidant enzyme activities and inhibits membrane lipid degradation by regulating energy metabolism has not been reported. In this study, the effect of 50 μmol L–1 MeJA treatment on energy metabolism was investigated in “crystal” grapes stored for 32 d. Its roles in the antioxidant properties and membrane lipids were also investigated. The results showed that MeJA treatment reduced the decay, weight loss, and browning index, inhibited the accumulation of soluble solids, improved the appearance of the fruit, and had a protective effect on crystal grapes. Compared with the fruit, MeJA-treated fruit stalks had higher adenosine triphosphate and adenosine diphosphate content and energy charge, as well as higher hydrogen ion ATPase, calcium ion ATPase, cytochrome C oxidase, and succinate dehydrogenase activities. During storage, MeJA stimulated glutathione production by activating dehydroascorbate reductase and monodehydroascorbate reductase activities, thereby maintaining total antioxidant capacity, free radical scavenging ability, ferrous reducing ability in the fruit. In addition, MeJA treatment inhibited the increase of phospholipase D, lipoxygenase, palmitic acid, and stearic acid; promoted the accumulation of phosphatidylcholine, linoleic acid, and arachidonic acid; and increased the unsaturated fatty acid/saturated fatty acid ratio. Therefore, MeJA maintained a higher energy charge level in grape stalks to varying degrees, slowed down the energy deficit, and inhibited oxidative stress and membrane lipid peroxidation processes in grapes, thereby reducing fruit deterioration and maintaining better fruit quality during storage.