The presence of oxygen vacancies (OVs) promotes persulfate activation. However, rational modulation of OVs without compromising the inherent structure of catalysts is challenging. Herein, novel OVs-enriched hollow ZnCo2O4 nanocages are synthesized based on a bimetallic ZIF-67@ZIF-8 precursor for efficient peroxydisulfate (PDS) activation. The incorporation of Zn into the lattice of Co3O4 boosts the number of OVs in the catalysts while preserving the morphology of Co3O4 nanocages derived from metal-organic framework (MOFs) templates. As a result, the degradation rate of organic pollutants such as bisphenol A is improved by over 20 times in the developed PDS activation system. OVs promote the formation of a surface-activated complex from PDS onto the catalyst surface, which can subsequently deprive electrons from pollutants. The developed PDS activation system is resistant to Cl−, NO3− and humic acid at environmental concentrations. This system adapts to selectively degrade organic pollutants with low ionic potential, and shows applicable potential in practical packaging wastewater treatment. The decreased catalytic performance of catalysts during utilization can be recovered with a facile thermal treatment. Our work constructs OV active sites on Co3O4 nanocages while preserving their original structural superiorities, providing a new strategy to functionalize MOF-derived materials.