During cooling of the ( R)-N-Fmoc-Octylglycine (Fmoc-OG)/cyclohexane solution, gelation is observed exclusively when ultrasound is used as an external stimulus, while deposit is obtained without sonication. The xerogel consists of entangled fibrous network made by interconnected nanofibers, while the deposit comprises large numbers of unbranched nanowires. It is found that the Fmoc-OG molecules form bilayer structures in both the deposit and the gel. However, the ratio ( R) between the Fmoc-OG molecules in a stable intramolecular H-bonding conformation and those in a metastable intermolecular H-bonding conformation can be tuned by the ultrasound, R (deposit) > R (gel). The increased population of the intermolecular H-bonding Fmoc-OG molecules induced by the ultrasonication facilitates to the interconnection of nanofibers for the formation of the fibrous network, and therefore gelation. The alteration in the morphologies and properties of the obtained nanomaterials induced by the ultrasound wave demonstrates a potential method for smart controlling of the functions of nanomaterials from the molecular level.