The interaction of atomically precise monolayer thiolate (SR) protected gold nanoclusters (Au NCs) with the phospholipid membranes has been studied by the all-atom molecular dynamics (AAMD) simulations. The effect of cluster size, type, and the surface charge density of protection ligand was studied. The simulation results show gold nanoclusters with different size and surface modifications have much different transmembrane behaviors. The Au25(SR)18 cluster was found to possess the best affinity to the phospholipid membranes among six atomically accurate clusters Au25(SR)18, Au36(SR)24, Au44(SR)28, Au68(SR)32, Au144(SR)60, and Au314(SR)96. Using the Au25 NC as a model, this work also found that the aggregation mode of the surface ligands and the surface charge density are the important factors affecting the interaction between the gold nanoclusters and the phospholipid membranes. Moreover, the balance of hydrophilic and hydrophobic ligands on the surface of Au NCs is beneficial to the high permeability.