Antimicrobial peptides have broad spectrum of antibacterial properties and are expected to become the better alternatives of antibiotics. Studies on the antibacterial mechanism can provide guidance for the design of new antibacterial peptides. No matter what kind of antibacterial mechanism, antibacterial peptides adsorb on the cell membrane firstly. In this manuscript, the molecular dynamic simulations were used to study the interaction between antimicrobial peptide BLFcin6 and five different membranes. For five kinds of cell membranes, the peptide combined with the surface of DPPC-CHOL membrane and POPG membrane rapidly, and tend to entered the hydrophobic interior of DPPC membrane. However, the peptide have little contact with POPC-CHOL membrane and POPC membrane. In terms of interaction energy, the peptide and POPG membrane have the strongest interaction, which mainly arise through the electrostatic interaction between the pepetide and the hydrophilic head of POPG membrane. For peptide and DPPC membrane, the interaction are mainly arise between the peptide and the hydrophobic tail of DPPC membrane. However, the peptide only combined with the surface of DPPC-CHOL membrane because of the effects of cholesterol. In the process of combination, the N-terminal Argnine residues contact with the cell membrane firstly, electrostatic interaction plays a key role in the process of peptide anchor in the cell membrane. The research explain why BLFcin6 peptide have antibacterial effect at the atomic level, which are the key residues, and also provide help for the further study of BLFcin6 peptide and its derivatives.