Yolk-like nano/microparticles with superparamagnetic iron oxide (SPIO) cores and hierarchical nickel silicate (NS) shells, designated yolk SPIO@NS, are fabricated by combining the versatile sol-gel process and the hydrothermal reaction, involving the coating of SPIO particles with SiO2 and transformation of the SiO2 shells into NS hollow spheres with hierarchical nanostructures. Various yolk/shell nanostructures with tunable NS shell thicknesses and SPIO core sizes are successfully prepared by controlling the experimental parameters. Au nanoparticles can be impregnated into the yolk-like microspheres in situ to form SPIO@NS/Au composite particles and the as-prepared magnetic nanocatalysts show good catalytic activity, using the catalytic reduction of RhB as a model reaction. This facile method can be extended to the synthesis of other encapsulated particles with yolk-like nanostructure.