Well-defined hexadecylamine (HDA) intercalated structures, either interdigitated layers, bilayers, or hybrid layers of both, in a confined space of highly functionalized layered (x-zirconium phosphates (alpha-ZrPs) have been prepared based on the two-step intercalation mechanism and these distinct intercalated structures can serve as a model system to investigate the interactions of two monolayers whose amphiphilic tails are adjacent to each other. At the first intercalation step, the electrostatic interaction between HDAs and alpha-ZrP is dominant and results in an interdigitated layer structure (d(001) = 3.0 nm) and the interdigitated layer is saturated at around Phi = 50%, where Phi is the weight fraction of intercalated HDAs in the intergallery of alpha-ZrP. For (D higher than 50%, the bilayer structure (d(001) = 4.3 nm) emerges due to further hydrophobic interaction between HDAs initially grafted to alpha-ZrP and unanchored HDAs and the relative fraction of the bilayer structure over the interdigitated layer increases with the increase in the intercalated amount of HDAs. The intriguing morphology of alpha-ZrP tactoids intercalated with HDAs in coexisting bilayers and interdigitated layers is observed by using microtomed TEM and the two-step intercalation has also been verified with TGA and FT-IR. Also, a structural transition from the bilayers to the interdigitated layers is monitored by using in situ synchrotron WAXS showing that the hydrophobically intercalated HDAs are selectively deintercalated at a relatively low decomposition temperature around 220 degrees C.