The interfacial-dependent self-organization of a chiral amino acid amphiphile is observed by atomic force microscopy (AFM). This chiral amino acid amphiphile possesses an amide group and two carboxyl groups that can form intermolecular hydrogen bonds in different forms, which corresponding to the two energy-minimum states exist in the aggregates of chiral molecules in one enantiomeric form. Three kinds of organizations were induced at different interfaces, which appear as helical aggregates on hydrophobic surface (e.g., highly oriented pyrolytic graphite (HOPG)), molecular flat layer, and superstructure layer on hydrophilic surface (e.g., mica). Moreover, these two energy-minimum states can also coexist in the same layer of the superstructure on an ordered hydrophobic surface made of the linearly aligned hydrocarbon chains. These phenomena experimentally prove the existence of double energy-mininium states in the chiral molecules that are in one enantiomeric form. The results presented here provide insight into how the interface can manipulate the bonding behavior in a multi-hydrogen bonding system and the self-organization of chiral molecules can be controlled consequently.