Molecular imprinting technique for the selective extraction of flavonoids from complex structural analog mixtures has attracted widespread attention in recent years. The molecularly imprinted polymers (MIPs) prepared by the conventional method has many disadvantages, which limits its application and development. In this paper, the research and application of five typical flavonoids (quercetin, rutin, isoquercitrin, puerarin, kaempferol) in molecular imprinting separation were summarized. The simulation, synthesis, characterization, application and optimization of MIP were discussed. The reversible addition-fragmentation chain transfer radical polymerization (RAFT) technique, magnetic functionalization, computer simulation, and optimization of solid phase extraction performance parameters can enhance the binding capacity, selectivity, mass transfer and separation of MIP imprinting. It points out the developed trend of developing new monomers, introducing new polymerization methods, improving the prepared efficiency of MIP, developing MIP for macromolecule detection, using MIP as microfluidic tool, proposing new configurations for synthesizing MIP, optimizing the rational design of MIP, and exploring large-scale synthesis methods of MIP. It can provide reference for molecular imprinting separation of flavonoids and their analogues.