Abstract In traditional Fenton-like reaction, both activation of peroxymonosulfate (PMS) and adsorption of pollutants were performed on the catalyst surface, leading to a competition. Obviously, this was not beneficial to maximize the function of catalyst with limited surface area. With this in mind, the spatial separation of functional sites was realized via constructing a yolk/shell nanoreactor made of MgSiO3 shell with high adsorption for methylene blue (MB) and Fe3O4 core with superior activity toward PMS activation. Therefore, the hollow void inside of Fe3O4@MgSiO3 nanoreactor provided a microenvironment for Fenton-like reaction. Their adsorption kinetics were satisfied with pseudo-second order kinetic and Langmuir model, and the maximum adsorption capacity was calculated to be 125 mg/g. According to the Boltzmann equation, the local MB concentration on shell was about 1.9 times higher than that in bulk solution. In Fenton-like reaction, radical concentration was high due to the confined space, and their diffusion distance was short owing to the small void of 25 nm. By taking advantage of synergistic effect established between adsorption process and Fenton-like reaction, the removal rate was about 1.5 times higher in comparison with that of Fe3O4 nanoclusters. In recycling experiment, 79.2% of removal efficiency still remained after five cycles. This study suggested that yolk/shell Fe3O4@MgSiO3 nanoreactor was a promising catalyst for Fenton-like reaction by which the removal of emerging contaminants could be greatly improved.