A microscopic understanding of chiral separation mechanisms in liquid chromatography is significant in the pharmaceutical industry to facilitate the rational design of novel stationary phases and the optimization of separation processes. A molecular simulation study is reported to investigate the chiral separation of racemic D/L-phenylglycines. Thermolysin crystal and water act as the chiral stationary phase and the mobile phase, respectively. D-Phenylglycine is observed to transport more slowly than L-phenylglycine, in accord with experimentally observed elution order. A slower flowing rate of the mobile phase enhances separation efficacy. From the energetic and structural analysis, it is found that D-phenylglycine interacts more strongly with thermolysin than L-phenylglycine; consequently, it stays more proximally to thermolysin for a longer time. The chiral discrimination Of D/L-phenylglycines is attributed to the collective contribution from the chiral centers of thermolysin residues. This study suggests that, as a bionanoporous material, thermolysin has enantioselectivity capability and demonstrates the feasibility of molecular simulations in mimicking enantioseparation processes and probing underlying mechanisms.