Cyclotides are disulfide-rich cyclic peptides isolated from plants, which are extremely stable against thermal and proteolytic degradation, with a variety of biological activities including antibacterial, hemolytic, anti-HIV, and anti-tumor. Most of these bioactivities are related to their preference for binding to certain types of phospholipids and subsequently disrupt lipid membranes. In the present study, we use a cyclotide, cycloviolacin O2 (cyO2), as a model system to investigate its interactions with three lipid bilayers 1-palmitoyl-2-oleoylphosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG)-doped POPE, and 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), to help understand its potential mechanism of action toward the membranes at the molecular level using molecular dynamics simulations. In our simulations, cyO2 repeatedly forms stable binding complexes with the POPE-containing bilayers, while within the same simulation time scale, it "jumps" back and forth on the surface of the POPC bilayer without a strong binding. Detailed analyses reveal that the electrostatic attraction is the main driving force for the initial bindings between cyO2 and the lipids, but with strikingly different strengths in different bilayers. For the POPE-containing bilayers, the charged residues of cyO2 attract both POPE amino and phosphate head groups favorably; meanwhile, its hydrophobic residues are deeply inserted into the lipid hydrophobic tails (core) of the membrane, thus forming stable binding complexes. In contrast, POPC lipids with three methyl groups on the amino head group create a steric hindrance when interacting with cyO2, thus resulting in a relatively difficult binding of cyO2 on POPC compared to POPE. Our current findings provide additional insights for a better understanding of how cyO2 binds to the POPE-containing membrane, which should shed light on the future cyclotide-based antibacterial agent design.