In this study, a new molecularly imprinted polymer chiral stationary phase (MIP-CSP) was prepared utilizing molecular crowding agent for improvement the selective separation ability. S-amlodipine (S-AML), methacrylic acid (MAA), ethylene glycol dimethacrylate (EDMA), and polymethyl methacrylate (PMMA) were selected as template, functional monomer, cross-linker, and molecular crowding agent, respectively. The composition of formulas for MIP-CSP was optimized, and the permeability and structural feature of resultant MIP-CSP were characterized. The effect of mobile-phase composition, including ionic strength, pH, and organic modifier content, was investigated for achieving the selective separation of rac-amlodipine (rac-AML) on MIP-CSP. The baseline separation of rac-AML was achieved with resolution of 1.58, whereas no selective separation was observed on the imprinted monolith without molecular crowding agent. The perturbation chromatography method was successfully applied to evaluate the recognition mechanism of templates on MIP-CSP. The retention time of S-AML detected in typical analytical conditions was obviously greater than the time of negative peak derived from perturbation, which indicated the retention of template may be due to the imprinted cavities on MIP-CSP. Additionally, the result of Van't Hoff analysis indicated that the chiral separation of rac-AML on MIP-CSP was an entropy-driven process, which supported the molecular imprinting theory. These results reveal that molecular crowding is a potential strategy for preparation of MIP-CSP with excellent selective separation ability. Graphical Abstract Improvement of chiral separation on molecularly imprinted monolith by molecular crowding condition.