Cobalt-based oxides are promising candidates for heterogeneous activation of peroxymonosulfate-based (PMS) advanced oxidation processes towards contaminants degradation, hence improving their catalytic performance is desirable requirement. Herein, an oxygen vacancy-rich flower-like CoMoO4 catalyst (CoMoO4-VO) assembled with nanosheets was successfully synthesized and applied for PMS activation to eliminate emerging contaminants. The CoMoO4-VO catalyst exhibits superior organic pollutants (e.g. sulfamethoxazole, SMX) removal performance with an apparent reaction rate of 1.29 min−1, which is much higher than that of the original CoMoO4 catalyst (0.30 min−1). Additionally, the catalyst also shows remarkable contaminants conversion in real river water, and even achieves more than 90 % of SMX degradation efficiency under a continuous flow reaction condition with a hydraulic retention time of approximately 2 min. The characterization and density functional theory (DFT) calculation results indicate that much electron accumulates around the formed oxygen vacancy on the surface of catalyst and transfers towards substrates. Meanwhile, the introduction of more oxygen vacancies could boost the adsorption of PMS as well as SMX, and the electron-donation capacity of catalyst, thus improving the generation of reactive oxygen species and the subsequent contaminate elimination. Radical quenching and capture experiments demonstrate that the enhanced degradation performance of CoMoO4-VO catalyst is attributed to the boosted radical pathway, especially for SO4− species, while scarcely contributed from the non-radical 1O2 species. This work provides an effective catalyst for contaminant elimination through PMS activation and deeply reveals the defect engineering-induced activity enhancement mechanism.