Whey protein isolate (WPI) has a variety of nutritional benefits. The stability of WPI beverages has attracted a large amount of attention. In this study, Flammulina velutipes polysaccharides (FVPs) interacted with WPI to improve the stability via noncovalent interactions. Multiple light scattering studies showed that FVPs can improve the stability of WPI solutions, with results of radical scavenging activity assays demonstrating that the solutions of the complex had antioxidant activity. The addition of FVPs significantly altered the secondary structures of WPI, including its α-helix and random coil. The results of bio-layer interferometry (BLI) analysis indicated that FVPs interacted with the WPI, and the equilibrium dissociation constant (K_D) was calculated as 1.736 × 10⁻⁴ M in this study. The in vitro digestibility studies showed that the FVPs protected WPI from pepsin digestion, increasing the satiety. Therefore, FVPs effectively interact with WPI through noncovalent interactions and improve the stability of WPI, with this method expected to be used in protein-enriched and functional beverages.