•MeJA treatment improved the cold resistance of green bell pepper.•MeJA treatment changed the membrane lipid component of green bell pepper.•MeJA treatment reduced CI of green bell pepper by regulating membrane lipid metabolism. The effects of methyl jasmonate (MeJA) treatment on membrane lipid metabolism of green bell pepper during cold storage was studied. The results showed that the chilling injury (CI) index, electrolyte leakage, malondialdehyde (MDA) content, phospholipase D (PLD) activity and gene expression of green bell pepper treated with MeJA were lower than those of the control fruit. MeJA treatment was able to maintain a higher level of ascorbic acid (VC) content, higher levels of phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS) and lower levels of digalactosyldiacylglycerol (DGDG), phosphatidic acid (PA), digalactosyldiacylglycerol/monogalactosyldiacylglycerol (DGDG/MGDG) and PC/PE compared to control fruit. In addition, MeJA treatment can also increase the proline content of green bell pepper fruit. Therefore, the reason that MeJA can improve the cold resistance of green bell pepper fruit may be attributed by the decreased expression and activity of PLD gene. The degradation of membrane lipid was delayed, and the content of proline increased, thereby maintaining cell membrane stability.