In order to understand the microscopic properties of alkylammonium-intercalated vermiculites, molecular dynamics simulations employing the clayff-CVFF force field were performed to obtain the interlayer structures and dynamics. The layering behavior of alkyl chains was uncovered. With the model used in the present study (1.2 e per unit cell), the alkyl chains formed monolayers with carbon-chain lengths of C6, bilayers from C7 to C10, and pseudo-trimolecular layers from C15 to C18. Intermediate states also existed between bilayer and pseudo-trimolecular layer states from C11 to C14. The ammonium groups had two locations: most ammonium groups were located over the six-member rings (~90%), and the rest above the substitution sites (~10%). The ammonium groups interacted with the vermiculite surface through H bonds between ammonium H atoms and surface O atoms. The ammonium groups were fixed firmly on surfaces and, therefore, had very low mobility. The alkyl chains were slightly more mobile. The similarities and differences between alkylammonium-intercalated vermiculites and smectites were revealed. The layering behaviors of alkyl chains were similar in alkylammonium-intercalated vermiculites and smectites: the alkyl chain behavior was controlled by both the amount of layer charge and the carbon chain length. The distributions of ammonium groups, however, were different, caused by the layer-charge distribution in vermiculites being different from that in smectites. The atomic-level results derived in the present study will be useful for future research into and the applications of organo-vermiculites.