As a prevalent Co-contained catalyst, modified Co3O4 has been widely utilized to activate peroxymonosulfate (PMS) for organic wastewater treatment due to its affordability and accessibility. While the catalysis enhancement of Co3O4 modified by catalytic inert species is often attributed to the formation of oxygen vacancies (OVs), the underlying mechanism beyond OVs remains unclear. Herein, we designed a one-pot pyrolysis process to synthesize ZnO/Co3O4 heterojunctions featuring Zn–Co tetrahedral coordination on their interface. In the PMS-advanced oxidation process for methylene blue (MB), the epitaxial growth of inert ZnO on the surface of Co3O4 led to an 88-fold increase in catalytic activity, facilitating the rapid degradation of organic dyes to achieve the deep mineralization of the effluent. Co sites and surface hydroxyls on the ZnO/Co3O4 heterojunctions played a crucial role in PMS activation, generating a variety of reactive oxygen species. Among these species, singlet oxygen (1O2) was identified as the dominant species responsible for MB degradation, with the assistance of a sulfate radical. Theoretical calculations demonstrated that the Zn–OH group was easier to activate than Co–OH through the polarization during PMS chemisorption. The activated Zn–OH groups served as novel active sites, participating in PMS activation in a nonradical way to generate partial 1O2. This study sheds new light on the effect of catalytic inert species (ZnO) on enhancing the catalytic activity of Co3O4, refining our understanding of the catalytic generation route of 1O2 in PMS activation.