In this study, we investigate the kaolinite surfaces and their interaction with β-d-glucose and cellobiose using density functional theory calculations. We found that their molecular adsorption energy on kaolinite depends on i) the characteristics of the kaolinite surfaces such as the hydroxylated (001) surface or the siloxane 001¯ surface and ii) a molecular orientation of the monomer on the surface. The adsorption energy of the β-d-glucose and the cellobiose on the hydroxylated (001) surface are significantly greater (almost 200%) than that on the siloxane 001¯ surface since the hydroxyl group can form hydrogen bond more efficiently than the oxygen in siloxane group. Through Mulliken population analysis, we found that the hydrogen bond formation induces charge redistribution of the kaolinite surfaces. Therefore, the hydroxylated (001) surface undergoes more significant charge redistribution due to more hydrogen bond formation with adsorbate molecules in comparison to the siloxane 001¯ surface.