Dodecyl dimethyl benzyl ammonium (DDBA) is a novel cation surfactant used to modify clay minerals. DDBA-intercalated montmorillonite is formed by the ion exchange between DDBA cations in the solution and cations in the montmorillonite interlayers. By using molecular dynamics simulations, we investigated the basal spacings, interlayer structures and dynamics of DDBA-montmorillonites. The results showed that the calculated basal spacings agreed well with experimental values and that the layering behaviours of DDBA had been revealed. The ammonium groups of DDBA ions preferred staying close to the centre of Si–O six-member rings. The benzyl group and lauryl group were oriented in parallel in the monolayer state, whereas they were tilted in other states. DDBA ions have very low mobility in the interlayer region, indicating that the negatively charged montmorillonite surfaces can effectively fix this positively charged surfactant. The microscopic structures and dynamics obtained in the present study provide atomic-scale insights into the properties of DDBA-intercalated clay minerals.