We report a morphotropic phase transformation in vanadium dioxide (VO2) nanobeams annealed in a high-pressure hydrogen gas, which leads to the stabilization of metallic phases. Structural analyses show that the annealed VO2 nanobeams are hexagonal-close-packed structures with roughened surfaces at room temperature, unlike as-grown VO2 nanobeams with the monoclinic structure and with clean surfaces. Quantitative chemical examination reveals that the hydrogen significantly reduces oxygen in the nanobeams with characteristic nonlinear reduction kinetics which depend on the annealing time. Surprisingly, the work function and the electrical resistance of the reduced nanobeams follow a similar trend to the compositional variation due mainly to the oxygen-deficiency-related defects formed at the roughened surfaces. The electronic transport characteristics indicate that the reduced nanobeams are metallic over a large range of temperatures (room temperature to 383 K). Our results demonstrate the interplay between oxygen deficiency and structural/electronic phase transitions, with implications for engineering electronic properties in vanadium oxide systems.