The separation of naphthol and methoxynaphthalene isomers was investigated by high-performance liquid chromatography on a RP-C18 stationary phase using S-β- cyclodextrin (S-β-CD) as mobile phase additives. Effects of methanol content of mobile phase on the separation of analytes were examined. The Chromatograms of the naphthol and methoxynaphthalene isomers show that baseline separations were achieved on a commercial RP-C18 stationary phase using S-β-CD in the appropriate methanol content of mobile phase. In this study, the structure of the complex of naphthol and methoxynaphthalene isomers with β-CD was calculated by theoretical calculation, and the difference of hydrogen bonding force was analyzed. The hydrogen bonding force between naphthol and S-β-CD plays an important role in the retention order.