Display omitted •A hierarchical Co3O4@Co3O4/Fe3O4 yolk-shell nanoreactor was designed and prepared.•The confinement effect and bimetallic cycles were integrated in this nanoreactor.•This nanoreactor could activate PMS for various organic pollutants degradation.•DFT calculations and MD simulations disclosed the confined reaction mechanisms. It is still a challenging task to reasonably design an efficient Co3O4-based nanoreactor for persulfate activation and accurately disclose the confined reaction mechanism. Herein, we design and prepare a hierarchical Co3O4@Co3O4/Fe3O4 yolk-shell nanoreactor (CT@CT/MG). In this yolk-shell structured nanoreactor, a Co3O4 solid sphere is the yolk and a flower-like Co3O4 hollow sphere wrapped by Fe3O4 nanoparticles is the shell. The void between them constitutes a confined space. Various instrumental techniques are used to characterize the structure and compositions of this nanoreactor. Degradation experiments show that CT@CT/MG have powerful capability to activate peroxymonosulfate (PMS) for the degradation and mineralization of various organic pollutants and even their mixture. Radical quenching experiments and EPR results confirm that •OH and SO4•− are the dominant reactive oxygen species in the CT@CT/MG-PMS system. Electrochemical measurements indicate that CT@CT/MG have better electron transfer ability and lower charge transfer resistance. In-situ characterization techniques including in-situ FT-IR and in-situ Raman are employed for deep insights into the potential reaction mechanisms. XPS analyses prove that Fe2+ promote the cycling regeneration of the reactive Co2+. MD simulations and DFT calculations disclose the confined reaction mechanisms by the means of comparative investigations in a confined space and under the unrestricted environment.