To do an extensive investigation of the chiral recognition mechanism of the molecular imprinting technique, two kinds of enantio-selective molecularly imprinted polymers (MIPs), N-tert-butoxycarbonyl-L-tryptophan (N-Boc-L-Trp) and N-tert-butoxycarbonyl-L-tyramine (N-Boc-L-Tyr), were synthesized by photo-induced and thermal-induced polymerization, respectively, and were employed as the stationary phase in liquid chromatography. A stoichiometric displacement model for retention (SDM-R) was successfully constructed and applied to evaluate the chiral separation of the MIPs. The simulation results showed that the values of ln k' in the proposed SDM-R could be employed to characterize the efficiency of the MIP's total separation, and the value of n could be used to denote the space effect of the enantiomers interacting with the MIPs when the interaction between the solutes and MIPs was a hydrogen-bonding interaction. Further studies showed that the suitability of the MIP cavity structure mainly determined the chiral-recognition ability of the imprinting system, when a strong hydrogen-bond competitive solvent was added into the mobile phase.