The two-dimensional (2D) molecular imprinting approach has attracted extensive research interest in recent years due to its potential advantages such as simple construction, fast template removal and rapid mass transfer. In this study, a new 2D imprinting approach based on the combination of mesoporous silica materials and molecular imprinting technology is reported. 2D molecularly imprinted materials (MIMs) for cholesterol were prepared by using cholesterol as the template, azide modified β-cyclodextrin (azide-β-CD) as the functional monomer and alkynyl-modified SBA-15 (alkyne-SBA-15) as the skeleton. In this method, azide-β-CD molecules were first assembled around the templates by formation of template-monomer complexes, and thus the mutual positions of azide-β-CD molecules were fixed. Then, azide-β-CD molecules were anchored to the walls of the nano-pores of SBA-15 via click chemistry. After removal of the template molecules, the resulting cavities, i.e., recognition sites were formed in the nano-pores of mesoporous silicas. The synthesized MIM was characterized by FT-IR, X-ray diffraction (XRD), elemental analysis (EA), thermal gravimetric analysis (TGA), scanning electron microscopy (SEM) and so on. Binding kinetic experiments demonstrated that the 2D imprinting approach can improve site accessibility for the template effectively. The 2D MIM exhibited binding affinity and specificity for the template, as revealed by equilibrium binding experiments. When using MIM as a stationary phase for HPLC, baseline separation of cholesterol from other compounds can be achieved. In addition, the use of 2D imprinting significantly reduced the peak broadening and tailing.