Two types of molecular-imprinted polymers-based magnetic chitosan with facile deep eutectic solvent-functional monomers (Fe3O4-CTS@DES-MIPs) were synthesized and applied as adsorbents in magnetic solid-phase extraction (MSPE) for the selective recognition and separation of (+)-catechin, (-)-epicatechin, and (-)-epigallocatechin gallate in black tea. The obtained Fe3O4-CTS@DES-MIPs were characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscopy. The selective recognition ability was examined by adsorption experiments. The actual amounts of (+)-catechin, (-)-epicatechin, and (-)-epigallocatechin gallate extracted from black tea using Fe3O4-CTS@DES-MIPs by the MSPE method were 13.10, 6.32, and 8.76mg/g, respectively. In addition, the magnetic Fe3O4-CTS@DES-MIPs showed outstanding recognition and selectivity. Therefore, it can be used to separate bioactive compounds from black tea. The new-type of DES adopted as the functional monomer in this paper provides a new perspective for the recognition and separation of bioactive compounds.