Beta cyclodextrin (βCD) is well-known as a potent drug carrier improving drug solubility, stability, and bioavailability. The water layer adjacent to the membrane surface and lipophilic domain itself are a controlling barrier for drug transport. However, the molecular details of the interaction between βCD and the lipid membrane has not yet been clearly explained. Here, molecular dynamics simulations were performed to visualize the interaction process of the βCD molecule with the lipid bilayer for six microseconds in total. Our results show that βCD passively diffuses into the lipid bilayer by pointing its open secondary rim toward the lipid polar groups and then remains at the phosphate and glycerol-ester groups with hydrogen bond formation. The information obtained from this study may suggest that the association of βCD at the cellular membrane plays an important role for the transfer of drug and the extraction of cholesterol.