Interlayer modification of layered materials with organocations has been known to endow the nanocomposite with hydrophobicity, and adsorption of aromatic compounds in the aqueous phase has been investigated for decades by using montmorillonite, a representative layered clay mineral, as the host material. Usage of the organocation has been believed to be effective due to the π-π interaction with the aromatic adsorbate, the presence of which is not verified spectroscopically in the water-immersed state. Considering that the organocation is generally regarded as a pillar to keep the interlayer space, the interaction between the organocation and adsorbate has not yet been clarified sufficiently. In the present study, we revealed the role of the organocation by the molecular dynamics method, where tetramethylammonium (TMA) and trimethylphenylammonium (TMPA) ions were selected as the representative and simple organocations, and benzene was the adsorbate to exclude the effect of the substitution group. Both H2O and benzene molecules were introduced in the interlayer of TMA- or TMPA-modified montmorillonite to model the water-immersed adsorption structure. It was found that H2O is preferentially distributed on the clay surface, followed by the center of the interlayer when the amount of H2O is large. In the adsorption model, benzene was vertically adsorbed on the clay surface. Radial distribution function analysis revealed that benzene is distributed around both the methyl and the phenyl groups in the TMA and TMPA cations, but the orientation of the phenyl ring is not consistent with that of benzene. Thus, benzene was found not to form the π-π interaction in montmorillonite modified with the TMPA cations in the water-immersed state. Furthermore, the surface was partly covered with the phenyl group in the TMPA cation, decreasing the adsorption area. Therefore, the experimental suggestion that benzene is adsorbed on the clay surface was reproduced by our simulation, and the interaction between the organocation and benzene and surface occupancy should be paid attention to maximize the adsorption property.