Biopolymer complexes fabricated by proteins and neutral polysaccharides have some specific and innovative functionalities. A better understanding of the interactions among these biopolymers might provide new insight into the applications of the complexes. Therefore, this study aimed to investigate the structural characteristics and molecular interaction mechanisms of whey protein isolates (WPI) and Auricularia auricular polysaccharides (APs). The turbidity analysis confirmed that the pH value and mixing ratio of the two polymers had strong effects on the formation of the APs-WPI complexes. All dispersions formed soluble complexes at approximately pH = 6.0 (pHc). APs-WPI self-assembles exhibited physically cross-linked networks under higher APs proportions, while they formed spherical complexes at higher WPI ratios. The addition of APs could alter the secondary structure of WPI, and the most noticeable changes were located in the regions of β-sheet and β-turn as confirmed by circular dichroism (CD) analysis. A molecular docking study showed that the amino acid residues of β-lactoglobulin complexed with the –COOH and –OH groups of APs. Hydrogen bonds and hydrophobic interactions, which were nonbonding contributions, played a key role in the formation of the APs-WPI complex. This study provided a basis for the development and application of APs in WPI-based beverages.