A simple method for controlling the pore structure and properties of ordered mesoporous silica (OMS) by the phys-isorption of organic molecules is reported. The paraffin-modified OMSs were characterized by N-2 gas and water vapor adsorption isotherms, small-angle X-ray scattering, and infrared spectroscopy. We found that paraffin first adsorbed on the pore surface defects, resulting in a smooth OMS pore surface; thus, the paraffin controlled the pore structure. In addition, the surface hydrophobicity increased with increasing paraffin filling fraction.