Deep eutectic solvents (DESs) were well known as new solvents because of their unique properties. Green DESs could be used as green, efficient, and economical extractants for the separation and purification of bovine serum albumin (BSA). In this study, FeCl3 & sdot;6H2O was used as a reactant to prepare four types of magnetic deep eutectic solvents (MDESs). In these MDESs, FeCl3 & sdot;6H2O was a hydrogen bond acceptor, while lactic acid, citric acid, acetic acid, and glycerol were hydrogen bond donors. Under simulated physiological conditions, the interactions between MDESs and BSA were investigated. Through fluorescence spectroscopy and series of calculations, the fluorescence quenching constants of the interaction between MDESs and BSA at different temperatures were analyzed, and the type of fluorescence quenching was determined to be static quenching; the binding sites were calculated, confirming that the 1:1 complexes were formed between MDESs and BSA; the thermodynamic parameters were calculated to clarify that the forces between them included hydrogen bonds, van der Waals forces, and electrostatic attraction; the binding rates of the MDESs-BSA system at different temperatures were calculated, and the ideal MDESs extractant for protein separation and purification was screened out. The results of circular dichroism spectroscopy measurement and calculation proved that after the addition of MDESs, the alpha-helix structure in BSA still dominates, further verifying that MDESs were extractants for protein separation and purification.