Different from their bulk counterparts, plasmonic molybdenum oxide nanomaterials display superior optical and electronic properties, but unfortunately, phase-controlled synthesis of molybdenum oxide nanomaterials with multifunctional performances still remains a challenge. To actualize this, a surfactant-free solvothermal strategy was proposed to fabricate molybdenum oxide nanomaterials with a tunable phase. Encouragingly, the as-prepared molybdenum dioxide nanoparticles (MoO2 NPs) exhibit intense near-infrared (NIR) absorption attributed to the localized surface plasmon resonance (LSPR) effect, which results in their application as a surface enhanced Raman scattering (SERS) substrate to detect trace amounts of molecular species including Rhodamine 6G (R6G), crystal violet (CV), IR-780 iodide (IR780) and methylene blue (MB). The detection limit was as low as 5 × 10-8 M and the maximum enhancement factor (EF) was up to 1.10 × 107, compared to other semiconductor nanostructures, the SERS sensitivity may be the best. Meanwhile, with the significant photothermal conversion efficiency up to 61.3%, the plasmonic MoO2 NPs could also be used as a photothermal therapy (PTT) agent for efficient photothermal ablation of cancer cells in vitro.