Paraquat, one of the most widely utilized herbicides globally, causes a significant environmental challenge due to its poor degradation rate and tendency to adsorb into clay interlayers. Several remediation methods have been proposed but their effectiveness remains suboptimal. The primary reason for this is the lack of microscopic understanding of paraquat–montmorillonite interactions. In this work molecular dynamics simulations were applied to study the interlayer structures and mobility of paraquat intercalated montmorillonite. Two stable hydration states were identified from the calculated immersion energy curve, which corresponded to a water content of 185 mgwater/gclay and 278 mgwater/gclay (the most stable). Paraquats remained in direct contact with the clay surface in both the anhydrous and hydrated states. At the water content of 185 mgwater/gclay, paraquats formed π-π stacking while at 278 mgwater/gclay, they were separated by a layer of water. Paraquat showed very small self-diffusion coefficients in the interlayer space of montmorillonite, indicating rather limited motions. The results in this work provide a basis for a better understanding of the interaction of paraquat with clay minerals.