AbstractTwo 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.