The aggregation behavior of a novel histidine derivative surfactant N-dodecanoyl-L-histidine (DHis) in aqueous solution was investigated. By mixing with cationic/anionic surfactant, an interesting phase transition over time from transparent homogeneous solution to jelly and finally to fibrous floccules was observed with aggregates growth taken place in the systems. Making use of the growing fibrous structures in the DHis/DTEAB and DHis/SDS systems as surface charge tunable dynamic template, we achieved sol-gel replication of silica and titania nanotubes in mild conditions, respectively. The possible mechanism underlying the formation of silica nanotubes was proved to be synergistically self-catalyzed hydrolysis and condensation of silica precursors depositing on the template surface. In particular, by optimizing the sol-gel process, silica nanotubes with tunable sizes in diameter and uniform wall thickness could be obtained in high yield. The large specific surface area and peculiar photoluminescence property of the silica nanomaterials indicated that the synthetic nanotubes were well-defined in both morphology and physical properties. Importantly, this fibrous aggregates could be universally used in opposite charged inorganic precursors to accomplish inorganic oxide nanotubes via sol-gel replication process, which may provide a general route for the construction of one-dimensional nanostructures in aqueous media.