Phospholipids (PLs), as natural additives and nutritional supplements, are recovered from the gum phase during the degumming process of crude vegetable oils. The molecular species of phospholipids recovered from crude soybean (SO), flaxseed (FO) and peanut oil (PO) by different degumming processes, including water (WD), acid (AD), PLA1(EDA), PLC (EDC) and PLA1-PLC (EDAC) were investigated. According to the PLS-DA model, a total of 30, 38 and 21 characteristic markers were identified using UPLC-Q-TOF-MS in the phospholipids recovered from SO, FO and PO by different degumming processes, respectively. PC (18:2/18:2) and PE (18:2/18:2) were the main phospholipids for WD and AD, LPC (18:2) and LPE (18:2) were the main phospholipids for EDA and EDAC, and PI (16:0/18:2) and PI (16:0/18:1) were served as characteristic phospholipids for EDC. In addition, a lamellar liquid-crystalline phase was observed in the recovered phospholipids, which indicated that the microstructure of phospholipids recovered from crude vegetable oils were significantly influenced by different degumming processes. These differential molecular species of phospholipid products provide useful information to facilitate the potential utilization of phospholipid products as emulsifiers in food and as ingredients in the pharmaceutical industries.