Animal proteins are good sources of protein for human, due to the composition of necessary amino acids. The quality of food depends significantly on the properties of protein inside, especially the gelation, transportation, and antimicrobial properties. Interestingly, various kinds of molecules co-exist with proteins in foodstuff, and the interactions between these can significantly affect the food quality. In food processing, these interactions have been used to improve the texture, color, taste, and shelf-life of animal food by affecting the gelation, antioxidation, and antimicrobial properties of proteins. Meanwhile, the binding properties of proteins contributed to the nutritional properties of food. In this review, proteins in meat, milk, eggs, and fishery products have been summarized, and polysaccharides, polyphenols, and other functional molecules have been applied during food processing to improve the nutritional and sensory quality of food. Specific interactions between functional molecules and proteins based on the crystal structures will be highlighted with an aim to improve the food quality in the future.