Oxygen vacancies were introduced into tungsten oxide (WO3) rods by irradiation with H2+, He+ or Ar+ ions and/or vacuum annealing. The surface chemical bonding states and visible light photocatalytic properties of these materials were subsequently assessed. Although the irradiated surfaces were contaminated with carbon and silicon species during ion irradiation, vacuum annealing at 500 °C decreased the extent of carbon contamination and increased the concentration of lattice oxygen species related to a surface WO3-x phase. The irradiated WO3-x rods exhibited low photocatalytic efficiencies during the degradation of rhodamine 6G compared with pristine WO3 rods, possibly due to the existence of contamination and oxygen vacancies. Vacuum-annealed WO3-x rods having a green coloration exhibited high photocatalytic efficiency as a result of enhanced visible light absorption and the low concentration of both surface contamination and vacancies.