Active ingredients of natural products are in low content and difficult to be enriched. It is very difficult to purify natural product by general methods due to the coexistence of macromolecules, small molecule interferences, isomers and molecules with similar structures. Molecular imprinting is promising in preparing highly selective separation matrixes. Molecularly-imprinted polymers (MIPs) show good prospect in the purification of active ingredients from natural products. In this review, the application of molecular imprinting technology in the separation and purification of active ingredients, such as alkaloids, steroidals, polyphenols, and flavonoids, from natural products is summarized, and our work in the extraction of shikimic acid is also introduced.