The purpose of this study was that the optimal hydrolysis conditions of endo- and exo-type enzymes were selected to utilize organic cheese byproducts. Optimal substrate concentration and optimum enzyme ratio were measured by using 4 kinds of endo-type enzymes (alcalase, neutrase, protamex, and foodpro alkaline protease) and two exo-type enzymes (flavourzyme and prozyme 2000P) for whey protein hydrolysis were analyzed using liquid chromatography. As a result, the optimal endo-type enzyme through the first enzyme reaction was selected as alcalse, and as a result of the secondary enzyme reaction, flavourzme was selected as the Exo type enzyme. The concentration of whey protein substrate for optimal primary and secondary enzyme reactions was 10%. In addition, the optimum ratio of enzyme was 0.5% of alcalase and 0.2% of flavourzyme, which showed low molecular weight chromatography pattern compared to 2% of alcalase and 1% of flavourzyme hydrolyzate. Therefore, hydrolyzing the endo-type enzyme alcalase at a concentration of 0.5% for 10 hours and then hydrolyzing the exo-type enzyme flavouryme at a concentration of 0.2% for 4 hours was considered to be the optimum condition.