A methodology for molecular dynamics simulation of alkaloid adsorption onto solid surfaces from solutions is developed by employing berberine as a model alkaloid, and water, methanol and N,N-dimethylformamide (DMF) as model solvents. A single berberine molecule and a solvation shell around it are considered as the solution model. The behavior of berberine at the vacuum-solid interface and at the solution-solid interface were simulated, and it is found that a berberine molecule adsorbed with its molecular plane parallel to the graphite surface is most stable, and the molecular conformation does not change considerably during dissolution in the solvents and adsorption onto the graphite. Also, the solvent effects on the adsorption are focused on by analyzing the potential energy change of berberine molecule being adsorbed onto the graphite surface from the solutions by molecular dynamics calculations, and discussed quantitatively by combining solvophobic theory and calculations of the potential energy by molecular simulation. It is known that the presence of water or methanol has little effect on the adsorption of berberine onto the graphite surface, and that the presence of DMF inhibits the adsorption of berberine significantly. It can be said that the methodology developed in this work is useful for studying the solvent effects on adsorption, and for choosing proper solvents in adsorptive separation and purification processes for alkaloids.