Magnetic nanoparticle (MNP) composites with a magnetite (Fe(3)O(4)) core and a hydroxyapatite (HAp, Ca(10)(PO(4))(6)(OH)(2)) coating were prepared using a precipitation method and a subsequent hydrothermal treatment. The hydrothermal treatment diminished the lepidocrocite layer on the magnetite, enhanced the crystal growth of HAp and dissolved the MNPs. The divalent iron ions dissolved into solvent were not substituted for the HAp lattice. The three-dimensional (3D) nanostructure, the crystal morphology of HAp covered with the MNPs and the interfacial nanostructure of magnetite/HAp were analyzed using an energy-filter transmission electron microscopy (EF-TEM) and visualized by computer tomography in transmission electron microscopy (TEM). EF-TEM and 3D reconstruction images using a tilted series of high-angle annular dark-field images showed that the needlelike HAp nanocrystals covered with a magnetite core and the crystal growth of HAp attached to the magnetite surface was inhibited as a result of the lower density of the nucleation site of the lepidocrocite layer. The dissolution of iron ion from MNPs and the interfacial interaction of HAp and magnetite could cause the needlelike morphology of HAp nanocrystals.