The synthesis of designed nanostructures is an ultimate target of nanomaterial science. Here, silica spheres with nanoholes have been selectively prepared. Coating the necklace-like structured and magnetic nanoparticles along carbon nanotubes, which is an essential step of the simple synthetic procedure of silica hollow spheres, led to the formation of silica hollow spheres with controllable sized nanoholes in their shell walls. The synthesized hollow spheres with nanoholes would be a good support for loading large molecules, e.g. drugs and proteins.