The controlled synthesis of ordered anionic surfactant templated mesoporous silica with cubic Ia3d̄ structure (AMS-6) is reported via prolonged periods of hydrothermal treatment (HT). The cubic Ia3d̄ mesophase transforms to hexagonal p6mm after 8 days of HT at 100 °C. Surprisingly, the hexagonal phase is stable only for a limited period after which a reversal to the cubic Ia3d̄ mesostructure is observed. Characterization methods such as powder X-ray diffraction (XRD), electron microscopy (SEM, TEM), N2-isotherms, magic-angle spinning (MAS) 29Si NMR spectroscopy, and thermogravimetric analysis (TGA) have been employed to follow structural and textural changes of the materials prepared. Data show that the resultant mesostructure and its textural properties are highly dependent on the period of HT with less unit-cell shrinkage on calcination after extensive HT. Furthermore, evidence of two different solid-solid phase mechanisms during HT is presented. The initial transition is consistent with a restructuring of the surfactant packing and a depletion of the organic moieties from the organo-silica wall as evident from 29Si NMR spectroscopy. The return to the bicontinuous cubic phase is driven by changes in charge matching at the organic-inorganic interface as a result of increases in the polymerization of the silica wall. The textural properties, and in particular the presence or absence of surface porosity, has been controlled through variations in hydrothermal treatment. These are associated with specific growth directions of cubic AMS-6 crystals. The synthetic method described allows us to easily prepare phase pure and intermediate mesostructured nanoparticles.