Hydroxyapatite (HA) with highly ordered three-dimensional pores, whose size is about 300 nm, was prepared by colloidal template method. The effect of the surface modification of silica spheres on the order degree of porous structure was investigated by field emission scanning electron microscopy (FESEM). Then, superparamagnetic Fe3O4 nanoparticles were fabricated via redox reaction, followed by coating with silica via a sol-gel process, in which a certain amount of TEOS was used in order to control the thickness of the silica shell. X-ray diffraction (XRD), transmission electron microscopy (TEM), and magnetometry were applied to characterize the properties. Finally, Fe3O4 magnetic nanoparticles coated with silica were adsorbed in the mesopores of HA with highly ordered three-dimensional pores by capillarity. The influence of dispersing agent on the adsorption results has been studied. Magnetometry was applied to characterize the magnetic properties of superparamagnetic HA. The quantities of adsorbed SiO2/Fe3O4 nanoparticles with core-shell have been compared by variation of saturation magnetization before and after adsorption.