As a layered photocatalyst, the photogenerated carriers separation efficiency of bismuth molybdate (Bi2MoO6) can be improved by introduction of oxygen vacancy. The alkali etching method provides a facile structural tuning way for modifying the bismuth-based semiconductors. Defect state bismuth molybdate (Bi2MoO6) photocatalyst was synthesized by alkali etching. The structure of Bi2MoO6 was tuned by adjusting the concentration of alkali solution. The phase structure, morphology, surface chemistry, and optical property of Bi2MoO6 were characterized by kinds of characterization methods such as X-ray diffraction, scanning electron microscope, X-ray photoelectron spectroscopy, UV–vis diffuse reflectance absorption spectroscopy. The phase of Bi2MoO6 can be transformed to Bi2O3 accompanied with the change of morphology due to the etching of molybdenum atom and oxygen atom from the Bi2MoO6 body structure by sodium hydroxide solution. Meanwhile, the concentration of oxygen vacancy increased obviously as indicated by the XPS results. Therefore, the separation efficiency of photogenerated carriers was enhanced because of the promotion of oxygen vacancy. Alkali etching Bi2MoO6 by 0.075 M sodium hydroxide solution exhibited an excellent photocatalytic performance owing to the suitable vacancy concentration. Superoxide free radicals instead of hydroxyl radicals took the important role in the photodegradation process.