Objective This study aimed to discuss the use of protein materials in formula food for special medical purposes to provide a reference for the selection of the protein materials, product registration management, and clinical use in the development and design of formula food for special medical purposes.Methods This study summarized and analyzed the requirements of the protein in terms of the regulations and standards, the characteristics of protein materials, and their use status in different types of formula food for special medical purposes from the perspective of evaluation.Results Protein plays an essential role in formula food for special medical purposes. The commonly used protein materials include whey proteins, casein and soybean protein isolates, hydrolyzed protein, and amino acids. Based on the different applicable people, proteins have different characteristics and clinical applications in nutritionally complete formulas, protein modules, and nutritionally complete formulas for a specific disease.Conclusion Following the current requirements of registration and standards and the literature review, studies on the characteristics of protein materials and human protein nutritional requirements are relatively well-established, but studies on proteins used in formula food for special medical purposes are still limited. Paying more attention to the basic research on the use of protein materials in formula foods for special medical purposes and the collection of data used in clinical studies is crucial.