Abstract: The interactions between drugs and bio-membranes play a key role in the in vivo behavior of drugs such as absorption, distribution, metabolism and elimination. Thus the clinical outcomes of drugs including both efficacy and side effects are directly related to the interactions of drugs and bio-membranes. Molecular dynamics simulations were used to study the drug-membrane systems, providing atomic details for optimization of chemical structure of drugs as well as drug delivery systems such as liposomes. Drug-membrane simulations from several aspects including bilayer membrane models, all atom and united atom models, coarse-grained models, and characteristic membrane properties were introduced. Several examples of drug-membrane simulations were also summarized.