Despite the extensive application of ellipsoidal micro-/nanoparticles, the synthesis of shape anisotropic ellipsoids is rare because of the minimization of surface free energy that favors simple spherical shape rather than complex nonspherical shape. We present the synthesis of silica ellipsoids with hexagonal mesostructure via the organic–inorganic cooperative assembly in the presence of cosolvents (KCl and ethanol). The aspect ratio of ellipsoids can be tuned systematically by controlling the concentration of ethanol. Transmission electron microscopy (TEM) shows that the ellipsoid possesses one-dimensional (1-D) pore channels parallel to the major axis, and the electron tomography (ET) technique shows that the ellipsoid has indeed hexagonal prism morphology in the middle and ellipsoidal morphology at two tips. A mechanism for the formation of mesoporous silica ellipsoids has been proposed. Importantly, magnetite/silica composite ellipsoids were prepared through a nanocasting route and can be used as building blocks to organize into ordered arrays in response to an external magnetic field. In addition, after functionalized with amino-groups, the amino-modified anisotropic magnetite/silica ellipsoids can be further used as carriers for delivering oligo-DNA-Cy3 into tumor cells, showing potential in directed self-assembly and drug/gene delivery.