There have been extensive studies on intercalation of alkylammonium into swelling clay minerals for the purpose of surface charge determination of the clay minerals, as well as their interlayer configurations in the clay minerals. The most accepted findings are that the intercalated alkylammonium molecules adopted horizontal monolayer, bilayer, pseudotrilayer, and vertical paraffin-like configurations in the interlayer space of the swelling clay minerals depending on the chain length and loading level of the alkylammonium used. This study examined the interlayer configurations of in alkyltrimethylammonium and their transition structure as a function of alkylammonium inputs and chain lengths. As the amount of alkylammonium intercalation increased, the bilayer configuration of the intercalated alkylammonium was absent during a transition from a horizontal monolayer to a pseudotrilayer intercalation. Instead, the transition structure involved a mixed layer made of rectorite intercalated with one layer and rectorite intercalated with pseudotrilayer of alkylammonium molecules. When in in horizontal monolayer, the alkylammonium molecules took a random, more gauche-like arrangement. On the other hand, as alkylammonium molecules adopted a pseudotrilayer. particularly the vertical paraffin-like arrangement, a more ordered all-trans configuration was achieved. As layer charge is one of the most important properties of swelling clay minerals, commonly determined by intercalation of n-alkylammonium ions, the identification of mixed-layer transition structure in this study may suggest a need for further investigations on principles of layer charge determination of swelling clays by the alkylammonium method.