Aggregation behaviors of the mixtures of lysine and fatty acids (FAs) with different chain lengths in aqueous solutions were investigated, and the self-assembled structural transition was determined in detail. Aggregates including micelles, vesicles, sponge structures, and fibers were observed by varying the compositions and the chain length of fatty acids. The sponge phase found in mixtures of octanoic acid and lysine was determined by freeze fracture-transmission electron microscope (FF-TEM). Circular dichroism (CD) signals were detected in the self-assembled structures due to the chirality of lysine molecules. The rheological properties of samples consisting of different aggregates formed by mixtures of lysine and fatty acids were measured, which provided the controlling factor of the chain length. The combined effect of noncovalent interactions including electrostatic interactions, hydrogen bonding, and hydrophobicity is supposed to be responsible for the aggregation behaviors, in which the hydrogen bonding acts as the main driving force in the self-assembled process.