Abstract: To frame the molecular simulation foundation in early stage evaluation for the design and evaluation of the cyclodextrin inclusions for poorly soluble drugs, the inclusion cases of cyclodextrin (α-,β- and γ- cyclodextrin) to artemisinins (dihydroartemisinin, artesunate, artemether and arteether) in vacuum were studied and the mechanisms for the binding energy differences were analyzed in term of atomic interaction. The molecular mechanics and molecular dynamics programs were employed to calculate the inclusion cases of cyclodextrins to artemisinins at molar ratio of 1∶1. The binding energy of each complex in vacuum was predicted.It was indicated that hydrogen bonding and van der Waals force are mainly attributed to the interaction force of cyclodextrin to artemisinin analogs in vacuum. Different interaction patterns resulted in varied binding energies. The peroxo bridges in the structure of artemisinin analogs may also play a role in stabilizing the inclusion complexes.