In present work, influences of molar fraction and acyl chain length of lipids on the interaction between cationic nanoparticles (NP) and the lipid bilayer have been investigated via coarse-grained molecular dynamics simulations. It is found that the participation of the anionic lipids improves the NP–membrane interaction; however in the case of PC/PG mixed membrane, the bending of the membrane is merely dependent on the increase of molar fraction of charged lipids in the heterogeneous membrane because of the relatively slow diffusion of lipids in the membrane and the repulsive effect between charged lipids against their further aggregation around the NP. Besides, it is also found that the acyl chain length of lipids plays a crucial role on the NP-induced structural variation and morphology transition of the lipid bilayer. As a charged NP attaches to the membrane, a thin DPPC/POPG membrane is more vulnerable to these extracellular disturbances than a relatively thick DSPC/DOPG membrane. Different from the NP-induced lipid eyelid structure budding from the DSPC/DOPG membrane, the adsorption of a NP disrupts the DPPC/POPG membrane and evokes a water pore in the lipid bilayer, implying the translocation mechanism of a NP across the membrane could be mediated by the acyl chain length of lipids. These results are beneficial for an further understanding in the translocation mechanism of nanocarriers as drug delivery vehicles for cancer therapeutics.