Silica–nickel–carbon composite microspheres with shelly hollow structures and tunable electromagnetic properties were prepared in large scale through a three-step route. Micron-sized precursor microspheres were prepared firstly by spray drying of water glass. Then a subsequent acid leaching with diluted hydrochloric acid was carried out to eliminate the Na₂O in the precursor microspheres to get single shell silica hollow microspheres (SHMs). Afterwards, Ni–C composite shells were assembled on the surface of the previously formed SHMs through a calcination route in an inert atmosphere to form silica–nickel–carbon composite shelly hollow microspheres (CSHMs) through decomposition of the reactants and carbon thermal reduction. By properly tuning the calcination conditions, silica–nickel CSHMs with gradients in composition can also be prepared. The electromagnetic properties of the CSHMs were studied and the results demonstrate that they present ferromagnetic and microwave absorbing properties related to the shell composition. The DSHPs thus obtained may have some promising applications in the fields of low-density magnetic materials and microwave absorbers. This work provides a new strategy to fabricate shelly hollow particles, which can be expected to be extended to the controlled preparation of similar structures with various compositions.