Gelatin and arabic gum were used as the wall material to prepare protease microcapsule with freeze drying technique through Box-Behnken design and response surface methodology. The microencapsulated protease were added to cheese to determine the ratios of pH 4.6 soluble nitrogen to total nitrogen and water soluble nitrogen to total nitrogen, as well as of 12% TCA soluble nitrogen to total nitrogen in ripened cheese. SDS—PAGE analysis, texture analysis and scanning electron microscope examination were also employed to analyze ripened cheese. It was shown from the analysis results that the optimum conditions for protease microcapsule preparation is that the concentrations of gelatin and arabic gum are 3.8% and 3.7% respectively, core material (protease) is 6.4mg/(100mL), and microencapsulation efficiency is 93.4%. The ratios of pH 4.6 soluble nitrogen to total nitrogen, water soluble nitrogen to total nitrogen, and 12% TCA soluble nitrogen to total nitrogen in ripened cheese are all increased when protease microcapsule is incorporated in cheese, indicated that degradation of casein into small peptides occurs and lead to the improvement in texture. The microstructure of proteins in cheese was destroyed after 60 days of ripening.