Tungsten trioxide (WO3) has the ability to transform oxygen-deficient structures (WO3-x; 0 ≦ x ≦ 1) at high temperatures under hydrogen. Because the band gap of WO3-x depends on the amount of W5+ species resulting from oxygen vacancies, this material is expected to have unique applications. Herein, to elucidate the WO3 reduction mechanism, we investigated the crystallographic changes of monoclinic WO3 powder samples using X-ray and neutron diffraction measurements under different reduction conditions, namely, under hydrogen at 500 or 800 °C for isothermal holding times of 30 min or 22 h. During heating, the yellow color of WO3 changed to various other colors, suggesting that WO3 underwent different reactions with hydrogen depending on the temperature and isothermal holding time. The X-ray powder diffraction results indicated that the hydrogen-treated WO3 crystals formed various oxygen-deficient structures, including stoichiometric WO3-x, non-stoichiometric WO3-x, and W metal. However, the formation of a single WO3-x phase was extremely difficult. For the blue WO3 sample obtained at short isothermal holding times, the total scattering analysis suggested that the oxygen vacancies in WO3 gradually formed at local positions. Furthermore, the neutron powder diffraction measurements revealed that the reduction of WO3 under hydrogen occurred on the surface. These results obtained by diffraction measurements enhance the knowledge in the chemical and physical properties of WO3-x.