Modification of food proteins by interactions with polyphenols has been used to improve the functional properties of proteins. In this study, soy isoflavones-whey protein complexes were prepared via non-covalent complexation. Solubility of soy isoflavones and changes in conformation and functionality of whey proteins were investigated. The results showed that the solubility of soy isoflavones was significantly increased by the complexation with whey proteins (p < 0.05). Soy isoflavones induced decreased α-helix and increased β-sheet of whey protein but increased α-helix and decreased β-sheet of polymerized whey protein. The solubility, foaming properties, and emulsifying activity of whey proteins were enhanced. The thermal stability of whey protein was decreased, but the thermal stability of polymerized whey protein was increased. The thermal gelation behavior of whey protein was enhanced. This study demonstrated that the conformation and functionality of whey proteins could be modified by interaction with soy isoflavones. There were some different changes in the functionalities of whey protein and polymerized whey protein due to the diverse conformation changes. The current study may provide useful information for the modification of whey proteins by polyphenols complexation.