The interaction between whey protein and acacia which were used as wall material was studied on the formation of the oils microcapsules by the FTIR Spectroscopy and Computer Aided Analysis. The results indicated that whey protein changed obviously in amide A and amideⅠ by high pressured homogenization and spray-drying. The amide A moved from 3 406.5 cm-1 to 3 425.4 cm-1 which was possibly due to covalent cross-linking between whey protein and acacia. Furthermore the amide Ⅰ moved from 1 648.6 cm-1 to 1 654.7cm-1 for intramolecular hydrogen bonding of protein had been weaken. After Gaussian fitting on amide Ⅰ, it was found that the content of secondary structure of α-helix content andβ-fol.ding in whey protein reduced from 19.55% to 17.50% and from 30.59% to 25.63%, respectively. This suggests that protein intramolecular hydrogen bonding force was abated, resulting in abating the rigid structure of the protein molecules and enhancing of the toughness structure. The protein molecules showed some flexibility. The result of SDS-PAGE electrophoresis showed that whey protein - gum Arabic complexes produced covalent products in larger molecular weight. During the spray-drying process, covalent cross-linking produced between whey protein and gum Arabic which improved emulsifying activity of the complex whey protein and gum Arabic produced covalent cross-linking and improved the complex emulsifying activity. Observing the surface structure of the fish oil microcapsule by SEM, the compound of whey protein and acacia as wall material was proved better toughness, less micropore, and more compact structure.