Abstract: As a functional material with a three-dimensional network structure, protein-based hydrogels are widely used in the food and biomedical fields. However, precisely regulating their properties and clarifying the structure-activity relationship remains a difficult task in current research. From the perspective of "structure-function synergistic regulation", this paper systematically reviews the classification system and formation mechanism of single protein, dual protein, and polysaccharide-protein composite hydrogels; deeply analyzes the synergistic effects and applicable boundaries of multiple preparation techniques such as heat treatment, ionic crosslinking, enzymatic crosslinking, and their combined methods; and systematically evaluates how to analyze the structure-activity relationship through key characterization techniques such as microstructure and mechanical properties. Finally, this review prospectively discusses the challenges and future development directions in emerging fields such as the precision delivery of bioactive compounds, 3D-printed foods, and intelligent drug carriers, with the aim of providing theoretical foundations and innovative perspectives for the design and development of high-performance protein-based hydrogels specifically tailored for food applications.