The storability of longan fruits of the “Fuyan” cultivar was investigated by subjecting them to 1-methylcyclopropene (1-MCP) treatment to delay membrane lipid metabolism in the pericarp during postharvest storage. After 1-MCP treatment, the activities of lipase, lipoxygenase (LOX), and phospholipase D (PLD) and the contents of phosphatidylcholine (PC), phosphatidylinositol (PI), and pyruvic acid (PA) in the pericarp were measured. Fatty acid components, such as oleic acid, linoleic acid, linolenic acid, myristic acid, palmitic acid, and stearic acid in the cell membranes of the pericarps were analyzed by HPLC-Q-TOF-MS/MS. Results indicated that with the prolongation of storage, the activities of lipase, LOX, and PLD in the control and experimental groups increased, whereas the contents of PC and PI decreased. Within zero to six days after harvest, the experimental group had higher activities of lipase, LOX, and PLD, higher contents of PC, PI, PA, oleic acid, linoleic acid, and linolenic acid, and lower contents of myristic acid, palmitic acid, and stearic acid compared with the control group, with differences being statistically significant (p < 0.05). Six days after harvesting, the activities of lipase, LOX, and PLD were 25.62 U/mg, 12.62 U/mg, and 0.80 U/mg, respectively, and the respective contents of PC, PI, and PA were 0.39 mg/g, 0.22 mg/g, and 0.52 mg/g in the experimental group. The results indicated that 1-MCP effectively reduced the activities of lipase, LOX, and PLD, promoting an increase in the contents of phospholipid components, such as PC and PI, and inhibited the production of the phospholipid degradation product PA in the longan pericarp during postharvest storage. This led to the inhibition of physiological metabolism in the cell membrane of the pericarp, thereby maintaining the stability of the cell membrane system and enabling the prolongation of the storage life of longan fruits.