The oxidative desulfurization (ODS) is a promising industrial technology of environmental protection, and developing effective catalysts for aerobic oxidation desulfurization (AODS) has attracted much attention. In this work, composite CoMoO4-Co3O4 hollow nanocages (CoMoO HNCs) are synthesized using a novel self-template strategy with ZIF-67 as the sacrificial template, and they show a superior ODS performance to eliminate the dibenzothiophene (DBT) completely at 110 °C in 1 h, O2 in air as the oxidant. The outstanding ODS activity is the outcome of large specific surface area (221.3 m2 g−1), high dispersed molybdenum active centers, causing more Mo to react with DBT in oil. The ODS mechanism of Mo-peroxo species based on O2 is proposed. Additionally, CoMoO HNCs catalysts can be easily separated by centrifuged and show excellent recycled stability. This work provides a valuable method for designing cost-effective Mo-based bimetal oxides catalysts with outstanding ODS performance for industrial applications.