The structure and dynamics of alkylammonium-intercalated smectites were simulated using molecular dynamics employing the clayff-CVFF force field, the reliability of which was firstly validated for these systems. The layering behaviors of alkyl chains confirm the scenarios of the monolayer, transition and bilayer configurations for short, medium-length and long carbon tails, respectively. In the systems without water, the alkylammonium groups are all anchored firmly above the surface six-member rings through H bonds between ammonium hydrogen and surface oxygen, and the alkyl tails are a little more mobile. With water involved, some ammoniums are dragged out of the potential barriers of the six-member rings by water molecules through the strong H bonds between water oxygen and ammonium hydrogen. The intercalated water scarcely affects the basal spacing, alkyl chain layering or alkylammonium dynamics. It is also found that the systems with alkyl chains of 11 to 14 exhibit the greatest density, resulting in the extremely limited mobility of the intercalated species.