Beta cyclodextrin (βCD) is well-known as a drug carrier which is able to enhance drug activity. It could increase the solubility of drug in an intermediate aqueous layer. However, the understanding of the interaction between βCD and lipid membrane referring to drug delivery improvement has not yet been clearly explained. To visualize the permeation of the βCD into the lipid bilayer, a microsecond of molecular dynamics simulations were performed with various starting configurations of βCD. We found that the βCD preferably located in the region between phosphate and glycerol-ester groups of lipid bilayer with the secondary rim pointing toward to the bilayer’s center. In addition, the free energy profile of βCD translocation through a lipid bilayer had been calculated by using umbrella-sampling technique. The result of free energy calculation was in good agreement with unbiased MD simulations. Our studies suggested that not only the improvement of water solubility by βCD inclusion but also the permeation behavior of βCD is essential i.e. the lipid head group is preferable location which implies to the βCD could potentially carry drug into lipid bilayer interior.