Grains are an energy source for human beings, and the two main components-starch and protein-determine the application of grains in food. The structure and properties of starch play a decisive role in determining processing characteristics, nutritional properties, and application in grain-based foods. The interaction of proteins with starch greatly affects the structure, physicochemical, and digestive properties of the starch matrix. Scientists have tried to apply this effect to create foods tailored to specific needs. Therefore, studying the effect of protein on the structure and properties of starch in the starch-protein complexes will help in designing personalized and improved starch-based food. This paper reviews the latest research about the effects of endogenous and exogenous proteins on the structure and properties of starch, as well as factors influencing the interaction between protein and starch. This includes investigations of the chain and aggregation structure of proteins with starch, as well as assessments of impacts on thermal properties, rheology, gel texture properties, hydration properties, aging, and digestion. In addition, particular examples illustrating the effects of protein-starch interaction on starch properties in various foods are discussed, providing a reference for designing starch-protein foods that are rich in terms of nutrition and easier to process.