A polypiperazine amide (PA) composite membrane was prepared by interfacial polymerization using a trimesoyl hexane solution as the oil phase and a piperazine aqueous solution as the water phase on a polysulfone ultrafiltration substrate. The surface was inspected by attenuated total reflection-Fourier transform infrared spectroscopy, showing that a polyamide layer was formed. The molecular structure of polypiperazine amide was simulated using Materials Studio as a plane molecule with hexagon rings of 1.5 nm in diameter of the inscribed circle. Incorporating the result of wide angle X-ray diffraction pattern, the supermolecular structure of the PA was predicted as an irregular laminated structure. This model appears good according to the performance of the membrane. Also investigated was the morphology of the membrane by scanning electron microscope, showing a dense layer of 300 to 400 nm on the porous substrate. The composite membrane obtained is a high-performance nanofiltration membrane.