The influence of the mobile-phase composition and temperature on the surface structure of the octadecylsilica (ODS) stationary-phase was investigated by applying a molecular-dynamics (MD) simulation. The molecular model to which the MD simulation was applied consisted of three parts: an amorphous silica base, dimethyloctadecylsilyl ligands and mobile-phase solvents. More detailed information on the effect of the mobile-phase composition was obtained by constructing larger molecular models than those used in our previous study. The thickness of the hydrocarbon layer of the stationary phase could be estimated based on the distance between the carbon atom located at the terminal end of the ODS ligand and the silica gel surface. The structural information obtained by the calculation showed good consistency with the experimentally observed values. The gauche fraction in the ODS ligand conformation could be also estimated to obtain a more detailed ligand conformation for each molecular model. It was found that as the temperature increased, the ligand conformation collapsed more. This trend was the same as the experimentally observed trends obtained by NMR, FT-IR, and Raman spectroscopic techniques.