The hydrothermal method is the most effective approach for the synthesis of VO2 metastable polymorphs with unique powder crystallite morphology. In this work, we expanded the capabilities of this method, directing it to the growth of oriented crystallites in self-organized systems on single crystal substrates. According to our investigations, a large variety of 3D structures of vanadium dioxide can be obtained using one single crystal substrate r-sapphire by fine tuning of synthesis parameters. The orientation growth of six-pointed vanadium dioxide crystallites fits into an epitaxial growth model describing unit cell relations between the VO2(M1) film and r-sapphire substrate. We describe the process of VO2(M1) phase stabilization in the films and the changes of resistivity and terahertz transparency of the films based on the metal–insulator transition (MIT).