Sample preparation was carried out for the removal of interfering substances in the complex matrix sample. Molecularly imprinted mesoporous silica (MIP-MS) is the specific adsorbent used in the sample preparation for solid-phase extraction. MIP-MS can increase the binding capacity, selectivity, and site accessibility of the molecular target. MIP-MS was synthesized using several materials, such as a silica precursor, surfactant, organosilane, functional monomer, and template molecule. Each material influences the formation and analytical performance of the MIP-MS. This review discusses the factors affecting the analytical performance in MIP-MS synthesis, such as the template molecular concentration, the ratio of the silica precursor and organosilane concentration, the type of functional monomer, and the functional monomer concentration. In addition, factors affecting the analytical performance in the adsorption-desorption study, such as pH, mass sorbent, eluting solvent, and washing solvent, to reach high-analyte recovery are also described.