Vanadium-containing polyoxometalates (POM) were synthesized by two distinct procedures (hydrothermal and under acidic conditions) and were thoroughly characterized by X-ray diffraction, Fourier transform infrared spectroscopy, Brunauer−Emmett−Teller (BET) method, UV−vis, 31P and 51V magic angle spinning NMR, scanning electron microscopy, and extended X-ray absorption fine structure spectroscopy-X-ray absorption near-edge spectroscopy (EXAFS-XANES). POM crystals were successfully grown under acidic atmosphere, thus forming a self-assembled structure constituted by cubic crystals that are between 20 and 80 μm in size. EXAFS-XANES experiments and molecular orbital calculations upon the Keggin unit cell allowed the determination of both the nature of the interactions and the assembly of the polyanions. A growth model was therefore developed based on the aggregation of Keggin units, ranging from one heteropolyanion unit to a crystal. Herein, we report a bottom-up approach which can serve as a powerful tool to assemble complex nanostructures via self-assembly, as well as to identify the building blocks present in solution during the assembly process. Finally, these auto-organized cubic vanadomolybdate crystals exhibit the highest catalytic activity and selectivity in the liquid phase partial oxidation of 2-methylnaphtalene into K3 vitamin.