•L. theobromae-induced disease development of longans concerns cell membrane damage.•L. theobromae induced higher activities of PLD, lipase and LOX in longan pericarp.•L. theobromae promoted the degradation of membrane phospholipids in longan pericarp.•L. theobromae lowered the contents of unsaturated fatty acids in longan pericarp.•L. theobromae raised the contents of saturated fatty acids in longan pericarp. Effects of Lasiodiplodia theobromae inoculation on disease development, pericarp browning and membrane lipids metabolism of harvested “Fuyan” longan fruit were studied. Compared with control fruit, L. theobromae-inoculated longans showed higher fruit disease index, pericarp browning index and cell membrane permeability, as well as higher activities of phospholipase D, lipase and lipoxygenase. Additionally, there were lower contents of membrane phospholipids but higher content of phosphatidic acid, and lower level of unsaturated fatty acids but higher level of saturated ones with lower ratio of unsaturated fatty acid to saturated fatty acid and lower index of unsaturated fatty acids in pericarp of L. theobromae-inoculated longans. These results suggested that L. theobromae-induced disease development and pericarp browning of harvested longans might be attributed to the damaged cellular membrane structural integrity, induced by the activated membrane lipids-degrading enzymes increasing the degradation of membrane phospholipids and unsaturated fatty acids in pericarp of harvested longan fruit.