A series of 2,2-diallyl-1,1,3,3-tetraethylguanidiniumchloride copolymers with N-vinylpyrrolidone (AGC-VP), vinylacetate (AGC-VA), and methacrylic acid (AGC-MAA) were obtained by free radical polymerization reaction. The guanidinium copolymers were loaded with silver nanoparticles, and there were investigated cytotoxic properties of the synthesized nanocomposites along with the features of interaction with model membranes (small anionic liposomes). The nanocomposites have a selective cytotoxic activity against cancer cell lines. Nano(AGC-VP) provokes a noticeable increase in cellular apoptosis in a dose-dependent manner and has great prospects as apoptosis inducer of A549 cells triggering only apoptotic cell death. All nanocomposites complexed with liposomes; herewith, the features of interaction with the lipid membrane were dependent on the composition of the copolymer in the nanocomposite. Nano(AGC-VA) had no destructive effect towards the liposomes and, in the case of Nano(AGC-MAA), negligible defect formation was observed. At the same time, Nano(AGC-VP) induced lateral segregation of lipids and formation of defects in the bilayer that resulted in irreversible interaction with liposomes. Detailed studies of the physicochemical aspects of liposome-to-nanocomposites interactions make it possible to understand the mechanism of action of composite materials, thereby bringing us closer to the possibility of practical application of the latter.