The phospholipid (PL) composition and milk fat globule (MFG) structure are important for MFG membrane function. However, the effects of various processing methods on these factors remain unclear. In the present study, we compared the effects of different processing methods for infant formula (IF) production on PLs and MFGs. Homogenization and heat sterilization significantly decreased the number of PL species in raw milk (RM, 104). Heat sterilization and spray drying significantly reduced PL content in RM (160.3 ± 12.2 mg/L; p < 0.05). During processing, the average volume diameter (5.67 ± 0.81 μm) and zeta potential (−7.37 ± 0.27 mV) of RM were significantly reduced (p < 0.05). After homogenization, PLs were distributed in a circular and dotted manner around the MFGs. After spray drying, PL fluorescent rings lost structural integrity. Therefore, the tested processing methods substantially damaged the PL composition and MFG structure. These results may provide a scientific basis for future IF development.