Leather biotechnology based on enzyme is one of the main directions toward clean technology in the leather manufacturing process. Proteins such as collagen, elastin, and keratin are important components in animal hides or skins, and proteases are most frequently used in the leather manufacturing process for the removal of interfibrillar substance and opening-up of collagen fiber instead of toxic chemicals. Elastin is an important and highly elastic structural protein in the animal hides or skins and significantly affects the properties of the final leather product. For improving the quality of leather product, thorough understanding of the mechanism of action of proteases on elastin is necessary. The action of proteases on elastin has been mostly studied either qualitatively by histological analysis or quantitatively based on substrate casein or stained substrates, such as congo red-elastin and Remazol Brilliant Blue R-elastin; however, the resulting products have not been accurately characterized and thus these methods are not up to the standard. Besides, controlling the hydrolytic action of proteases to elastin has been very difficult, and excessive hydrolytic action of protease damages the elastin, restricting the wide application of proteases in the leather manufacturing process. In order to quantitatively evaluate the hydrolytic action of proteases on elastin in a more accurate manner, in this study, a new method was established by determining the unique amino acid desmosine based on the covalently bonded elastin-desmosine conjugate. Quantitative analysis of desmosine was performed in liquor based on cowhides substrate, and qualitative characterization was accomplished by histological analysis of elastic fiber in hides using an optical microscope. The results of this study indicated that the newly developed method is sensitive, accurate, and reproducible. In addition, the unhairing trials also demonstrated the suitability of newly established method in the leather manufacturing process to evaluate the action of proteases on the elastin in animal hides or skins.