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Enzyme-assisted aqueous extraction processing (EAEP) has long been considered as a promising alternative to traditional solvent oil extraction, which has gained increasing attention recently. After EAEP of soybeans, three distinct layers are formed: cream, skim and residual fraction. The skim fraction contains substantial amount of protein as well as oil, sugar and other impurities. In order to recover value from this liquid fraction, ultrafiltration was employed for protein concentration and isolation. To investigate the interrelationship between operating parameters and membrane flux, Box-Behnken response surface methodology was introduced. The results indicated that the three factors’ effects on membrane flux followed the decreasing order as: solution mass fraction, transmembrane pressure and solution pH value. The improved regression model was fitted with determination coefficient of 0.9975 and optimal factors were as follows: operative pressure of 0.20MPa, solution mass fraction of 5.60%, and solution pH value of 8.50. The permeate flux under above conditions was 7.02L/(m2·h) and protein purity was increased to 88.63%. The infrared spectrum and HPLC analysis showed evidently characteristic peaks of functional groups in soybean protein and remarkable low levels of undigestible oligosaccharides. Besides, the protein extracted from EAEP showed improved solubilities especially at acidic pH value, but it slightly decreased emulsifying activity index and emulsifying stability index. Further improvement can be achieved if industrial fractionation unit was employed and process optimization was conducted. A complete costeffectiveness analysis would also need to be done to estimate the economic viability of this application.