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The synergistic diagnosis and treatment of tumors have become a developing trend in cancer treatment. Optical diagnosis and therapy with low toxicity, high efficacy, and safety have attracted wide attention. However, because of the poor water solubility and rapid clearance of imperfect materials, the clinical use of phototherapy is still hindered. Molybdenum oxide nanomaterials, as important transition metal oxides, have become a hot topic in nanomedicine in recent years since they can carry with oxygen to form a variety of molybdenum oxides (MoO
x
, 1 <
x
≤ 3) and show a variety of special morphologies, structures, and properties. Because of their special defect structure, molybdenum oxide nanoparticles show strong optical absorption in the visible and near-infrared region. On the other hand, their low biological toxicity, ease of excretion, and capability of photoacoustic imaging make them good photothermal material. In this review, we emphasize recent progress on the principle and research status of phototherapy based on molybdenum oxide nanoparticles in terms of chemical synthesis, mechanism, and future prospects.