Oxygen vacancies (OVs) have an important effect on the geometry, electronic structure and chemical properties of manganese dioxide (MnO2). In this article, we prepared alpha-MnO2 nanowires with different OVs concentration through a gas-assisted hydrothermal method. The crystal structure and morphology of samples were investigated with the aid of X-ray diffraction (XRD) and scanning electron microscope (SEM). Through introducing different reaction atmospheres in the hydrothermal reaction process, the amount of OVs in MnO2 nanowires was adjusted and confirmed using X-ray photoelectron spectroscopy (XPS). Pseudocapacitance of MnO2 nanowires was tested using a three electrode system. The theoretical calculation and experimental results demonstrated that the increase of oxygen vacancies could narrow the energy level and enhance the conductivity of alpha-MnO2, further lead to the improvement of the capacitance performance. Compared with MnO2 prepared in the air and oxygen atmosphere, the samples synthesized in the hydrogen environment had a relatively high concentration of oxygen vacancies and considerably high pseudocapacitance value of 136 F/g at 1 A/g current density.