This study aimed to investigate the structural changes in heat-induced polymerized whey protein (PWP)-fucoidan (FCN) hydrogels with different FCN concentration (0 % to 0.75 %, w/v). The interaction of PWP and FCN were traced by simultaneous rheology and Fourier transform infrared spectroscopy spectra (SR-IR) technology. The particle size and absolute zeta potential of PWP-FCN increased significantly (p < 0.05) with higher FCN concentrations, indicating that the formation of PWP-FCN enhanced the stability of the system. The gelation time of PWP-FCN was shortened from 1328 s to 881 s as the FCN concentration increased from 0 to 0.75 % (w/v) paralleled the increased apparent viscosity. The endothermic peak temperature of the hydrogels increased from 95.28 °C to 102.26 °C demonstrating the improved thermal stability due to FCN. The intrinsic fluorescence, surface hydrophobicity, and free thiol groups of PWP-FCN all indicated that FCN could interact with PWP through hydrophobic interactions, which changed the tertiary structure of PWP, and increased the density of PWP-FCN network. Cryogenic scanning electron microscopy (Cryo-SEM) and SEM images showed that the interactions between PWP and FCN resulted to rough and wrinkled microstructure of samples. Results of SR-IR and molecular docking assay both indicated that FCN could also interact with PWP through hydrogen bonds. In summary, FCN could promote the gelation process and the physicochemical properties of PWP-FCN hydrogel. Results of this study could provide theoretical basis for the application of protein–polysaccharide hydrogels in food field.