Previous studies indicated that the deep eutectic solvent (DES, also referred to as an ionic liquid analogue) regenerates wool keratin as an eco-friendly approach. However, the regenerated keratin still exhibited hydrophobicity, similar to other ionic liquids hence not conducive for further use. Herein, both water-soluble and non-water-soluble keratins were separated and studied to explore the differences between them for the first time. Our results showed that the content of obtained products increased with treatment time and rose in temperature with the main one being the non-water-soluble keratin. The FTIR spectra, NMR spectrum along with crystallinity analysis suggested that water-soluble keratin had a more α-helical structure, although it had a lower molecular weight as demonstrated by the SDS-PAGE data. The thermogravimetric analysis indicated that the more α-helical structure of water-soluble keratin contributed to poor heat resistance compared to the non-water-soluble keratin. Additionally, the amino acid analysis results indicated that the water-soluble keratin had a higher ratio of the number of amino acids with hydrophilic side groups to the number of amino acids with hydrophobic side groups compared to that of the non-water-soluble keratin. Collectively, we demonstrated that water-solubility could be due to the loose structure with a short peptide chain and hydrophilic groups, and the content of water-soluble keratin increased with treatment time and rose in temperature. This study adds to the body of knowledge on the use of regenerated keratin and further explores the mechanism of wool dissolution in ionic liquids particularly DESs.