We performed FEP and MD simulations on enantiomeric complexes of seven 18-crown-6 ether compounds and a chiral protonated amine to obtain the free energy differences, and to elucidate the mechanism responsible for enantioselectivity. The FEP calculation reproduced the experimental enantioselectivity quite well. We partitioned the binding free energy in solution into the binding free energy in the gas phase and the solvation energy, and discussed the results. In the MD simulations, the detailed motion of host-guest complexes was monitored.