Enzyme inactivation is vital in fruit and vegetable juice processing, and selective inactivation is a major focus of enzyme inactivation. We used electrospray treatment to investigate directional enzyme inactivation in cabbage juice. Peroxidase and polyphenol oxidase in cabbage juice are the enzymes causing deterioration, whereas myrosinase is a beneficial enzyme. The particle size distribution, zeta potential and secondary and tertiary structures of the enzyme proteins were evaluated before and after enzyme inactivation. After the electrospray treatment, the relative activities of peroxidase, polyphenol oxidase and myrosinase in the mixed-enzyme simulation system were 4.09%, 5.62% and 84.67%, respectively, and those in the cabbage juice were 6.68%, 5.24% and 77.34%, respectively. Additionally, electrospray treatment induced substantial aggregation of peroxidase and polyphenol oxidase in the mixed-enzyme solution, and the secondary and tertiary structures of peroxidase and polyphenol oxidase were destroyed. Moreover, the conformation of myrosinase was preserved. These findings indicated that electrospray treatment can cause selective inactivation of peroxidase and polyphenol oxidase while preserving myrosinase activity.