The complexation between negatively charged sodium dodecyl sulfate (SDS) and positively charged amphoteric polyurethane (APU) self-assembled nanoparticles (NPs) containing nonionic hydrophobic segments is studied by dynamic light scattering, pyrene fluorescent probing, zeta-potential, and transmission electron microscopy (TEM) in the present paper. With increasing the mol ratio of SDS to the positive charges on the surface of APU NPs, the aqueous solution of APU NPs presents precipitation at pH 2, around stoichiometric SDS concentration, and then the precipitate dissociates with excess SDS to form more stable nanoparticles of ionomer complexes. Three stages of the complexation process are clearly shown by the pyrene I1/I3 variation of the complex systems, which only depends on the ratio of SDS/APU, and demonstrate that the process is dominated by electrostatic attraction and hydrophobic aggregation.