Molecular imprinted polymers (MIPs) were prepared through thermal polymerization by using quercetin as the template molecule, acrylamide (AA) as the functional monomer and ethylene glycol dimethacrylate (EDMA) as the cross-linker in the porogen of tetrahydrofuran (THF). The synthesized MIPs were identified by both Fourier transform infrared (FTIR) and scanning electron microscope (SEM). Systematic investigations of the influences of key synthetic conditions, including functional monomers, porogens and cross-linkers, on the recognition properties of the MIPs were conducted. Scatchard analysis revealed that the homogeneous binding sites were formed in the polymers. Besides quercetin, two structurally similar compounds of rutin and catechol were employed for molecular recognition specificity tests of MIPs. It was observed that the MIPs exhibited the highest selective rebinding to quercetin. Accordingly, the MIPs were used as a solid-phase extraction (SPE) sorbent for the extraction and enrichment of quercetin in cacumen platycladi samples, followed by HPLC-UV analysis. The application of MIPs with high affinity and excellent stereo-selectivity toward quercetin in SPE might offer a novel method for the enrichment and determination of flavonoid compounds in the natural products.