Defected surface modification of metal oxides and hybridization of two crystal phases have been a good strategy of improving a catalytic performance by creating more active sites. Herein, MoO3, Mo3O9 center dot H2O and their hybrid microrods were synthesized by the hydrothermal method, and the corresponding defect induced structures were prepared by the post hydrothermal treatment. The fundamental physiochemical properties were fully elucidated by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction crystallography, Fourier transform infrared spectroscopy, Raman, UV-visible absorption spectroscopy, photoluminescence, and X-ray photoelectron spectroscopy. It was demonstrated that the hydrogen evolution reaction (HER) activity of the defect-induced hybrid MoO3/Mo3O9 center dot H2O microrods was dramatically enhanced by 100 x, compared with other structures. On the basis of the experimental results, induced defects, coupled oxidation states of Mo5+ and Mo6+, and the hybrids were shown to play crucial roles in the enhancement. The present defect modification in the hybrid structure could be a very useful strategy of improving catalytic activity in various catalyst application fields.