The pure α-MoO3 microflakes grown by the Chemical Vapor Deposition (CVD) technique are annealed at various temperatures (150 °C, 250 °C, and 350 °C) in a hydrogen (H2) atmosphere to induce ferromagnetism. All the samples exhibit ferromagnetism at room temperature, and the 250 °C annealed sample shows the highest magnetization of 0.087 emu/g. The presence of oxygen vacancies, verified through the analysis of X-ray photoelectron spectroscopy (XPS) and the Electron Probe Microanalyzer (EPMA) data, was found to be the main cause of the origin of ferromagnetism. A one-to-one correspondence is found between the concentration of oxygen vacancies and the magnetic moment, which is corroborated by first-principle-based calculations. The study suggests that the incorporation of H in the MoO3 matrix and the formation of HxMoO3 and MoO2, are other factors that influence ferromagnetism.