The invention provides a hollow silicon magnetic microsphere, as well as the preparation method and the application thereof. The preparation method comprises the steps as follows: a polystyrene/silicon dioxide composite microsphere is used as a core; Fe3O4 coats the periphery of the core through the layer-by-layer self-assembly method; then, a PS/SiO2/Fe3o4 polymeric magnetic composite nanosphere is obtained, and polystyrene is removed through the high temperature sintering method, thereby forming a magnetic material with hollow structure; the inner layer of the hollow magnetic material is SiO2, and the stability is good, thereby the material is not easy to collapse at high temperature; furthermore, the specific surface area of the material can be improved, and the material is a monodisperse hollow magnetic microsphere material. The method has the advantages of low cost and good repetitiveness. The obtained product not only can be used as a magnetic targeting drug carrier material, but also can be used in the biological and the medical fields such as biosensors, immunologic diagnosis, drug delivery and tumor targeting therapy as well as DNA isolation, etc.