A molecularly imprinted polymer (MIP) has poor site accessibility to the target molecule because the functional groups are embedded with a high cross‐linking density in a polymer matrix. In recent years, molecularly imprinted mesoporous silica (MIP‐MS) has been studied to overcome the drawbacks of MIP. MIP‐MS uses mesoporous silica as a support material; it has a large surface area, large pore size, an abundance of surface functional groups, and stable physical and chemical properties. MIP‐MS can increase selectivity, binding capacities, and the specific recognition ability and provides good stability. Many techniques have been developed for synthesizing MIP‐MS to increase its advantages. MIP‐MS has been used for sample preparation and extraction of analytes in various samples. We provide an overview of the methods for synthesizing MIP‐MS; factors that affect synthesis and application in sample preparation; and extraction of analytes in pharmaceutical, environmental, and food samples. In the end, we provide future perspectives on the study of this material.