Enhancing the surface-enhanced Raman scattering (SERS) activity of semiconductor metal oxide nanostructures by controlling the morphology and oxygen vacancies towards trace detection of organics is of significant interest. In this study, MoO₃ with a novel sea urchin morphology is synthesized employing chemical bath deposition and consists of hundreds of ∼15 μm long spikes originating from the core forming 20–40 micron globular structures. The spikes taper to form 20 nm sharp tips. SERS of rhodamine 6G (R6G) over MoO₃ sea urchins has been investigated and compared to that of 1D h-MoO₃ nanorod arrays. The SERS activity is morphology dependent and the sea urchin-like morphology exhibits higher SERS activity with an enhancement factor (EF) of the order 10⁵ and a detection limit of 100 nM, while for h-MoO₃ nanorods, the corresponding values are 10³ and 1 μM, respectively. X-ray photoelectron spectroscopy reveals a high concentration of Mo⁺⁵ states in sea urchins indicating lattice oxygen vacancies. The observed EF is quite high for a metal oxide substrate and is attributed to the enhanced charge transfer between analyte molecules and the substrate promoted by the oxygen vacancies along with surface defects and hydroxyl groups on MoO₃ sea urchins providing more active sites for the adsorption of probe molecules. The role of oxygen vacancies is confirmed by the lower EF value exhibited by the stoichiometric 1D h-MoO₃. Raman mapping of a single sea urchin is achieved with good R6G intensity and indicates that the tips of spiky features are involved in SERS enhancement. The reusability of substrates is shown for repeated cycles of R6G adsorption by UV irradiation exploiting the photocatalytic activity of MoO₃ nanostructures.