The manufacturing processes for infant formula disrupt the structure of phospholipid-coated milk fat globules, thereby impacting the physical stability of the system. In this study, either soybean phospholipids (SPs) or egg yolk phospholipids (EYPs) were incorporated into the milk system to reduce this damage, and their effects on the stability and fat globule structure of processed milk were examined. The findings revealed that the addition of phospholipids improved the physical stability and fat globule structure of different processed milk. In pasteurized milk, the stability constant of samples with phospholipids decreased from 0.42 to 0.37 compared to phospholipid-free milk, but no significant difference was found between the EYP and SP groups. In homogenized milk, adding EYPs resulted in a smaller particle size (870.35 nm versus 953.39 nm) and stability constant (0.28 versus 0.30) than the addition of SP. Moreover, homogenized milk added with EYPs exhibited a denser phospholipid interface film which led to a more intact fat globule structure. Consequently, the milk powder particles in the spray-dried milk supplemented with EYPs showed a more uniform distribution and smoother surface. These findings suggested that EYPs were superior to SPs in restructuring fat globules and enhancing newly formed fat globule stability during milk powder processing. This offers valuable insights for improving the physical and structural properties of dairy products, such as infant formula.