Methyl jasmonate (MeJA) is an important bioactive metabolite in fruits and vegetables that regulates various physiological processes. The effects of MeJA on pericarp browning in longan fruit and its underlying mechanism were investigated. Results showed that treatment with 100 μM MeJA substantially suppressed the development of pericarp browning in harvested longan fruit. Compared to untreated fruit, MeJA-treated fruit exhibited reduced cell membrane permeability during storage. Meanwhile, MeJA-treated fruit displayed lower levels of phosphatidic acid and higher content of phosphatidylcholine, phosphatidylinositol, phosphatidylglycerol, and phosphatidylethanolamine through suppressing the activities of key enzymes involved in membrane lipids metabolism, such as phospholipases, lipase and lipoxygenase. Furthermore, MeJA treatment enhances the energy status of the fruit, evidenced by elevated the levels of adenosine triphosphate and energy charge. This effect could be attributed to the enhanced activities of various energy metabolism enzymes. Overall, all results suggest that MeJA is a promising agent for inhibiting pericarp browning in longan fruit through modulation of membrane lipid and energy metabolisms.