Computational simulation and Doehlert experimental optimization were done for the rational design of a core-shell molecularly imprinted polymer (CS-MIP) for use in the highly selective separation of Tanshinone IIA (TSIIA) from the crude extracts of Salvia miltiorrhiza Bunge (SMB). The functional monomer layer of the polymer shells directed the selective occurrence of imprinting polymerization at the surface of silica through the copolymerization of vinyl end groups with functional monomers and also drove TSIIA templates into the formed polymer shells through the charge-transfer complex interactions between TSIIA and the functional monomer layer. As a result, the maximum rebinding capacity was achieved with the use of optimal grafting ratio by the Doehlert design. The CS-MIP exhibited high recognition selectivity and binding affinity to TSIIA. When the imprinted particles were used as dispersive solid phase extraction sorbents, the recovery yield of TSIIA reached 93% by a one-step extraction from the crude extracts of SMB, and the purity of TSIIA was larger than 98% by HPLC analysis. These results show the possibility of a highly selective separation and enrichment of TSIIA from the SMB using the TSIIA-imprinted core-shell molecularly imprinted polymers.