We have proposed a structural transformation method in Mo-doped In₂O₃ nanotubes (Mo-In₂O₃ NTs), by electron-beam irradiation with a high-resolution transmission electron microscope. Uniform Mo-In₂O₃ NTs have been presynthesized by a facile electrospinning method and calcined in air at 600 °C. As is expected, a large number of ultrafine nanoparticles gradually generate on the surface of Mo-In₂O₃ NTs after a few minutes of exposure to 300 kV electrons, which are further confirmed to be the crystal structure of nonstoichiometric MoO_x. This approach may be meaningful for us to design some novel nanostructures and has the potential to direct nanofabrication and emerging nanodevices.