Molecular simulation was used to study the interaction between template molecule and functional monomer to shorten the optimization time for the functional monomer and the ratio of functional monomer and template molecule.Kaempferol molecularly imprinted polymerization (MIP) monolithic column was therefore synthesized by reversible addition-fragmentation chain-transfer (RAFT) polymerization with dibenzyltrithiocarbonate (DBTTC) and ethyleneglycoldim ethacrylate (EDMA) as RAFT and cross-linking agent, respectively, whereas methacrylic acid (MAA) was the optimal functional monomer with the molar ratio of kaempferol/MAA of 1∶4 from molecular simulation results.The results indicate that molecular simulation is useful to simplify the experimental procedure, and DBTTC as RAFT agent can provide more adjustable and better MIP monolithic column.