Gold nanoparticles (AuNPs) are of biomedical importance, such as delivery vectors. Therefore, we used all-atom molecular dynamic simulations to study the interaction of AuNPs with cell membrane (DMPC bilayer). We observed that the AuNPs adhered spontaneously on the surface of the cellular membrane from the bulk phase, largely as a result of the AuNP-DMPC headgroup attraction. We calculated the potential of mean force for transferring an AuNP through a DMPC bilayer. It was observed that a high energetic barrier to AuNP was inserted into the hydrophobic core of the bilayer. The inclusion of AuNP induced local bilayer deformation and slowed fluidity of the lipid molecules in the vicinity of it. As the size of the AuNP increased, the lipids in the vicinity of the AuNP had larger local deformation and slower fluidity. We found that a nanoparticle-membrane complex was formed by the AuNP and its neighbor lipids. These neighbor lipids moved laterally together with AuNP. On average, they moved significantly more slowly than the other lipids. The nanoparticle-membrane complex not only provided a clue for endocytosis mechanism regulating the translocation of AuNPs across the cellular membrane but also helped us to better understand the endocytosis process.