Chiral stationary phases (CSPs) and molecular structure of enantiomers are two independent but related aspects in enantioseparation, which are discussed on the basis of the experimental data from the previous study. Two enantioseparation experiments are performed to illustrate the relationship between enantiomer structures and chiral stationary phases, one is the resolution of mandelic acid derivatives and the other is about prasugrel. Thermodynamic mechanism and theoretical study with computational chemistry method is helpful to understand the interactions of enantiomer and CSPs.