Abstract: In order to explore the thermal protective effects of different proteins on betanin and clarify its protective mechanism, two animal proteins-lactoferrin and β-lactoglobulin, and two plant proteins-rice protein and soybean protein isolate were used. The formation and interaction mechanism of protein-betanin complex were characterized from turbidity, UV spectrum, particle size, and molecular simulation. The results showed that all the four proteins could improve the thermal stability of betanin, the protective effect was: Lactoferrin>soy protein isolate>β-lactoglobulin≈rice protein. The improvement of the thermal stability of proteins to betanin was related to the formation of protein-betanin complex. The results of turbidity, UV spectrum and particle size experiments suggested that the affinity of betanin with lactoferrin, β-lactoglobulin and soy protein isolate was higher than that of rice protein, which might be caused by the low solubility and tight structure of rice protein. In addition, the results of interaction and molecular docking showed that lactoferrin and betanin were mainly bound through hydrogen bond and electrostatic interaction, hydrogen bond played a dominant role in the interaction between β-lactoglobulin and betanin, the main interaction between rice protein and betanin was hydrophobic interaction, and soy protein isolate bound to betanin mainly by hydrogen bond and electrostatic interaction. This study provides a theoretical basis for protein-natural pigment interaction and the research of protection of betanin.