Molecular dynamics (MD) simulation was conducted to explore the extraction mechanism of Cs+ and Na+ ions in the octanol–water biphasic system containing the ionophore: dicyclohexano-18-crown-6 (DCH18C6). The rate of phase separation for the Na+NO3 − system was rapid as compared to Cs+NO3 − and mixed metal ion systems. Further, the binding energy during complexation of Na+ cation is −55.86 kcal/mol which was found to be more than that of Cs+ ion (−31.23 kcal/mol). A large sharp peak height for radial distribution function in both Cs–CE and Na–CE complexes suggests a high stability and a strong interaction. The self-diffusion coefficient of the Cs+–CE complex (0.054 × 10−9 m2/s) at the octanol–water interface was found to be smaller than that of other species. © 2017 Taylor & Francis.