Different secondary structures of the pep-1 protein were blamed for transmembrane internalization process of drugs and drug deliveries. But which structure will be important for transmembrane delivery was still not clear. In this study, interactions between pep-1 and cell membranes were studied. Pep-1 in the buffer (Pep-1) and pep-1 on graphene (PDS/G) or they on graphene oxide (PDS/GO) were composed as the transmembrane delivery system to study the different secondary structure of pep-1 that influence for their transmembrane delivery. The curves of chirascan circular dichroism (CD) and all-atom discontinuous molecular dynamics (DMD) simulations illuminate that, in a buffer environment, most pep-1 formed 3-10 helix structures. Meanwhile, when Pep-1 composed graphene slice and formed PDS/G, 3-10 helix and alpha-helix structures can be found in small quantities. When they on graphene oxide and formed PDS/GO, coil or type II beta-turn structure can be found from most of the pep-1 and 3-10 helix structure disappeared. By using sum-frequency generation (SFG) vibrational spectroscopy, we found that pep-1 with 3-10 helix structures in buffer solutions damaged the lipid bilayer violently. PDS/G with less 3-10 helix structures will change the orientation of lipid bilayer effectively but slightly. Pep-1 with coil or type II Beta-turn in PDS/GO cannot influence the structure of lipid bilayers. Hemolysis experiments also proved that when pep-1 composed as PDS/G, they will change the orientation of the plasma membrane of red blood cells effectively but slightly. When they attach on the GO and formed PDS/GO, the plasma membrane of red blood cells cannot be influenced. In conclusion, 3-10 helix structures will be positively correlated with disturbance of membranes. These results will be effectively guided the clinic application of pep-1 as a transporter of the drug delivery system.