Proteins and polyphenols are important bioactive components in food systems, and their interactions have become an effective strategy for enhancing food functionality. This review systematically summarizes the molecular mechanisms by which protein-polyphenol interactions enhance the physicochemical properties, oxidative stability, sensory characteristics, bioactivity, and nutritional functionality of foods. It presents an overview of the mechanisms and influencing factors of protein-polyphenol interactions, focusing on recent advances in their applications in functional food ingredients, texture modification, active packaging, and nutrient delivery systems. By elucidating the intrinsic relationship among structure, function, and application, this review provides a theoretical basis and technical pathway for modern food processing and quality improvement.