Nanomaterial drug delivery systems have become one of the most important targeted therapy technologies. Although great efforts have been made to study the self-assembled mesoscopic structure of nanoparticles and understand drug loading and release mechanisms, the interaction between nanoparticles and cell membranes has not yet been clearly studied. Moreover, the research of experimental methods in this field has been greatly restricted due to its special time-space scale, so it is necessary to apply computer simulations to visualize the cell internalization of the nanoparticle. This review covers modelling methods and the current status and viewpoints of research on the influencing factors of the nanoparticle-biomembrane interaction mechanism. In particular, we discussed in detail the positive and negative effects of various nanoparticle properties. This article may assist researchers in rationally optimize the nanoparticle structure to improve therapeutic efficiency.