In this study, whey protein isolate-inulin (WPI-In) conjugates with varying degrees of glycosylation (DG) were prepared, characterized, and examined for their potential immunomodulatory effects and regulation of gut microbiota in mice. The data indicated that an increase in DG significantly affects the microstructure and functionalities of WPI-In conjugates. The WPI-In conjugates with high DG promoted the growth and development of the thymus while altering gut microbiota composition by increasing the relative abundance of