The simultaneous rational optimization of structure and composition is extremely important for improving the catalytic performance of yolk–shell nanoreactors, but has been rarely achieved so far. In this work, yolk–shell Co₃O₄/C@SiO₂ nanoreactors (YSCCSs) are facilely synthesized by coordinating the growth of Co-zeolitic imidazole framework (ZIF-67) crystals with the hydrolysis/condensation of tetraethoxysilane (TEOS). In this process, the preliminarily formed ZIF-67 crystals play an essential role in the final structure of YSCCSs, which can be used as the template for silicon hydroxide growth and the precursors for carbon and cobalt species. To present the advantages of YSCCSs as a catalyst, sulfate-radical-based advanced oxidation processes (SR-AOPs) for bisphenol A (BPA) degradation were chosen as the model reaction. For comparison, three other catalysts, including yolk–shell Co₃O₄@SiO₂ nanoreactors (YSCSs), and Co₃O₄ and ZIF-67 derived Co₃O₄/C nanoparticles, were also tested. The results show that YSCCSs exhibit significant BPA degradation performance over YSCSs, and CO₃O₄ and Co₃O₄/C nanoparticles. This outstanding catalytic performance is ascribed to the rational optimization of the catalyst from the following two aspects: (i) confinement effect of yolk–shell nanostructure and the improved dispersity of carbon supported Co₃O₄ species enhance the catalytic activity and stability (structure optimization); and (ii) the existence of graphitized carbon accelerates the electron transport from the catalyst to peroxymonosulfate (PMS) and thus increases the reaction kinetics (composition optimization). The results of this research show that metal–organic framework (MOF)-derived nanoreactors with a rational structure and composition have a promising application prospect for environmental remediation.