Mesostructured silica synthesized using cetyltriethylammonium (CTEA) ion as the pore-directing agent in acidic environments was ready to have interfacial anions exchanged at ambient temperature. In situ techniques including small-angle X-ray scattering (SAXS) and optical microscopy were used to examine the structural and morphological changes of the as-made mesostructured materials, and pyrene fluorescence quenching experiment was used to probe the variation in interfacial environment during the anion-exchange processes. About one-half of the interfacial anions between the silica framework and micelle were exchanged based on the fluorescence quenching experiments of pyrene, which was dissolved in the hydrophobic core of the micelle. Altering in the pore structure and the architecture of the silica framework was observed when the interfacial anions were exchanged by anions of higher salting-in power. The resultant phase transformation and morphological change were always toward pore structures of lower curvature. The influence of anion follows the Hofmeister series commonly encountered in macromolecular and biological systems. The mesophase transformation induced by the interfacial anion exchange provides a unique technique to study anions which are not yet included in the Hofmeister series.