Antimicrobial molecules from insects may serve as a potentially significant group of antibiotics. To identify the effect of antimicrobial peptides (AMPs) on bacterial membrane and obtain further insight in the mechanism of membrane transport of AMPs, the interaction of surface potential and permeation of a novel antimicrobial peptide MDpep5 (Val-Glu-Ser-Trp-Val) from Chinese traditional edible larvae of housefly was examined using liposomes from bacterial lipids extract. Compared with the cationic AMPs, MDpep5 cannot completely disrupt membrane. The uptake of MDpep5 by bacterial liposomes was dependent on the membrane surface potential. The mutual inhibition of the transport of MDpep5 through the cell membrane was caused by the change in surface potential due to the binding of MDpep5 to the membrane. Furthermore, formation of MDpep5-enriched lipid aggregates could lead to the disorder of the bilayer structure. Based on our experimental data, we propose that MDpep5 initiated its antimicrobial activity by profoundly disordering the structure and affecting physical properties of bacterial membrane when binding to the phospholipid which accounts for its bactericidal activity.