An efficient method is described for the preparation of phase-pure columnar mesoporous silica nanosystems within the channels of anodic alumina membranes (AAM) via evaporation-induced self-assembly (EISA). Upon the basis of a systematic investigation of the effects of interfacial interactions and different synthesis parameters on the resulting hierarchical mesophase, a salt-induced phase transformation was developed for efficient structural control. Samples with a columnar hexagonal 2D structure along the vertical channels of the AAM can be produced with ionic CTAB as template. However, when nonionic surfactants (Pluronic P123 and Brij 56) are used, samples with a circular hexagonal 2D structure perpendicular to the channels or phase mixtures of circular and columnar orientations are obtained. The behavior of ionic CTAB can be mimicked by adding inorganic salt to the nonionic template precursor solution, thus leading to a phase transformation toward columnar orientation. The distribution between the orientations was determined by means of small-angle X-ray scattering (SAXS) experiments. The effects of other synthesis parameters were also investigated, including temperature, surfactant: silica ratio, and salt composition. Strikingly, calcination-stable mesoporous materials with a columnar orientation exhibiting high mesoporosity and specific surface area were obtained for the first time with such structure directors. The salt-induced phase transformation is an efficient means for achieving a desired hierarchical mesostructure in the confined space of the AAM channels.