The aim of this study was to examine the effect of whey protein isolate (WPI) on the digestibility and physicochemical properties of potato starch (PS) after heat treatment. WPI reduced the digestibility of PS and increased the order and aggregation structure of gelatinized PS. Examination of the rheological properties of the PS-WPI mixed system before and after adding different chemicals (sodium chloride, urea, and sodium dodecyl sulfate) indicated an involvement of hydrogen bonds and hydrophobic interactions in the PS-WPI gelatinization system. The pasting properties, swelling power, and thermal properties indicated that WPI suppressed the swelling and gelatinization of PS. The addition of WPI reduced the amylose leaching rate from the starch granules, indicating that the presence of exogenous protein could prevent amylose diffusion from the starch granules. Native WPI and its hydrolysate also inhibited amyloglucosidase activity. These findings indicated that the mechanism by which WPI reduces PS digestion involves hydrophobic interactions and hydrogen bonding between WPI and PS, as well as enzyme activity inhibition.