Two new peptide-based isomers containing cholesterol and naphthalic groups have been designed and synthesized. We found that the position of L-alanine in the linker could tune the gelation properties and morphologies. The molecule with the L-alanine residue positioned in the middle of the linker (1 b) shows better gelation behavior than that with L-alanine directly linked to the naphthalimido moiety (1 a). As a result, a highly thermostable organogel of 1 b with a unique core–shell structure was obtained at high temperature and pressure in acetonitrile. Moreover, the gels of 1 a and 1 b could undergo an instantaneous gel-to-gel transition triggered by sonication. Ultrasound could break the core–shell microsphere of 1 b and the micelle structure of 1 a into entangled fibers. By studying the mechanism of the sonication-triggered gel-to-gel transition process of these compounds, it can be concluded that ultrasound has a variety of effects on the morphology, such as cutting, knitting, unfolding, homogenizing, and even cross-linking. Typically, ultrasound can cleave and homogenize π-stacking and hydrophobic interactions among the gel molecules and then reshape the morphologies to form a new gel. This mechanism of morphology transformation triggered by sonication might be attractive in the field of material storage and controlled release.