Aggregate structure, phase transition and their relationship to the preparation conditions of single chain Schiff base containing ammonium amphiphiles with different alkyl chains in aqueous vesicle bilayer were studied with differential scanning calorimetry, X-ray diffraction and electronic absorption spectrum. The experimental results showed that the bilayer structure existed in aqueous solution was affected by the length of tall alkyl chain. The amphiphile with a dodecyloxy tail could form both paralell and interdigitated structures. By controlling the preparation condition one of these two stacking form could be obtained as the main structure.