The organic small molecules like basic amino acids (BAA) arginine, lysine and histidine have been extensively used in the food protein modification for the improved functional properties. The introduction to the structures of BAA and their physicochemical characteristics, the inherent structures food protein and the exerting functional roles in the food systems as well, has been fully reviewed. In particular, the impact of BAA on the modifications of structures and functionalities (hydration, emulsifying and gelling properties) of a variety of protein sources in the common food systems and the potential mode of action(s) of BAA modifying proteins involved in them also have been systematically illustrated. Moreover, it is stressed that the lack of research orientation, relevant novel techniques and prospects in the functional improvement of plant-derived proteins and other representative mass food proteins by employing BAA. This review is intended to provide a reference for the full understanding of the theory for BAA modifying proteins and extend the utilization of BAA in foods.