The invention relates to a molecularly imprinted polymer, in particular to the molecularly imprinted polymer (MIP) prepared by adopting bulk thermal polymerization by taking genistein as template, tetrahydrofuran as opening agent, 4-vinyl pyridine as functional monomer and ethylene glycol dimethacrylate as crosslinker. The molecularly imprinted polymer takes on high compatibility and selectivity to genistein and daidzein in moving phase of acetonitrile-water mixture. The invention has the advantages that the prepared molecularly imprinted polymer takes on high compatibility and selectivity togenistein and daidzein in moving phase containing water, which ensures that as a selectivity parting material, the molecularly imprinted polymer has broad applying prospect in the aspect of separation and preparation of genistein and daidzein in herbal medicine.