Peptide amphiphiles readily self-assemble into a variety of nanostructures, but how molecular architectures affect the size and shape of the nanoaggregates formed is not well understood. From a combined TEM and AFM study of a series of cationic peptide surfactants A(m)K (m = 3, 6, and 9), we show that structural transitions (sheets, fibers/worm-like micelles, and short rods) can be induced by increasing the length of the hydrophobic peptide region. The trend can be interpreted using the molecular packing theory developed to describe surfactant structural transitions, but the entropic gain, decreased CAC, and increased electrostatic interaction associated with increasing the peptide hydrophobic chain need to be taken into account appropriately. Our analysis indicates that the trend in structural transitions observed from A(m)K peptide surfactants is opposite to that obtained from conventional monovalent ionic surfactants. The outcome reflects the dominant role of hydrophobic interaction between the side chains opposed by backbone hydrogen bonding and electrostatic repulsion between lysine side chains.