Understanding the interaction of ions with fatty acids is important to identify their roles in various bioprocesses and to build novel biomimetic systems. In this study, the molecular organization of palmitic acid (PA) films on alkaline buffer solutions (pH 7.4) with and without divalent Ca2+ was measured at a constant surface area using Langmuir troughs coupled with microscopy and X-ray interfacial techniques. Without Ca2+, PA molecules remained a monolayer organization; however, with Ca2+, formation of the inverted bilayers of PA-Ca2+ superstructures caused a spontaneous 2D to 3D transformation under no compression due to the strong interaction between PA and the divalent cation. Self-assembly of this highly-organized inverted bilayer superstructure involved a two-step process of nucleation and nuclei growth. During nucleation, densely packed PA and Ca2+ monolayer firstly corrugated and some of PA and Ca2+ molecules ejected out from the monolayer; the ejected molecules then reorganized and formed the inverted bilayer nuclei. Nucleation was followed by nuclei growth, during which PA and Ca2+ in the monolayer kept integrating into the inverted bilayer structure through molecule migration and PA rotation around Ca2+.