The burgeoning need to study the applications of nanoparticles (NPs) in biomedical and pharmaceutical fields requires an understanding of their interactions with lipid membranes for further in vivo studies. In this paper, negatively charged egg yolk lecithin liposome (EYL) has been prepared and used as model lipid membranes. Positively charged Mg3Al-layered double hydroxides (LDHs) are viewed as models of clay particles. The ability of the LDH NPs, a two-dimensional nanostructure with an average diameter of 100 nm (LDHs-100) or 500 nm (LDHs-500) to cross the membranes, has been thoroughly investigated via (high-resolution) transmission electron microscopy (TEM), optical microscopy (OM), scanning electron microscopy (SEM), confocal fluorescence microscopy (CLSM), and dynamic light scattering (DLS). The liposomes with an average diameter of 1.5 μm were prepared by the thin-film rehydration method followed by an extrusion technique. A calcein leakage assay and steady-state fluorescence measurement displayed the variation of membrane integrity and polarity of the pyrene-located microenvironment during the interaction between EYL and calcein-interacted LDH NPs (CE-LDHs) or LDH NPs, respectively. These results imply that not only spherical particles but also even more sophisticated nanostructured materials are able to effectively cross the lipid bilayers, thereby engineering new compounds that may be encapsulated for safe and potential use in biomedical applications.