A calculation approach to discuss the solvent effect on liquid phase adsorption has been developed by using the molecular dynamics simulation method and solvophobic theory. The distinctive feature of the approach is that the calculations of the potential energy changes related to the solvent effect can be achieved on the basis of the molecular structure only, without using any experimental physicochemical al property of the solute. This approach is applied to adsorption of five berberine alkaloids contained in Coptis japonica Makino onto the graphite surface from six solvents. Detailed analysis of the potential energy changes due to the solvent effect derived by molecular dynamics calculations yields an outline of the relative adsorption capacities of the alkaloids. Furthermore, the prediction of the preferential adsorption of alkaloids onto a graphite surface from the liquid phase and the eluent strength of solvents for desorption of the alkaloids from graphite surface were obtained. The calculated results are in good agreement with experimental data.