Nucleation and growth of SBA-15 silica nanostructured particles with well-defined morphologies has been followed with time by small-angle X-ray scattering (SAXS) and ultrasmall-angle X-ray scattering (USAXS), using synchrotron radiation. Three different morphologies have been compared: platelets, toroids, and rods. SEM observations of the particles confirm that two key physical parameters control the morphology: the temperature and the stirring of the solution. USAXS curves demonstrate that primary particles with a defined shape are present very early in the reaction mixture, immediately after a very fast nucleation step. This nucleation step is detected at 10 min (56 °C) or 15 min (50 °C) after the addition of the silica precursor. The main finding is that the USAXS signal is different for each type of morphology, and we demonstrate that the difference is related to the shape of the particles, showing characteristic form factors for the different morphologies (platelet, toroid, and rod). Moreover, the size of the mesocrystal domains is correlated directly with the particle dimensions and shape. When stirred, aggregation between primary particles is detected even after 12 min (56 °C). The platelet morphology is promoted by constant stirring of the solution, through an oriented aggregation step between primary particles. In contrast, toroids and rods are only stabilized under static conditions. However, for toroids, aggregation is detected almost immediately after nucleation.