Lipid-shelled nanobubbles have shown great potential in drug and gene therapy. To improve our understanding of the ultrasound-mediated interactions of lipid nanobubbles with plasma membranes at the molecular level, we investigated the effect of shock-induced lipid nanobubble collapse on a lipid bilayer using coarse-grained molecular dynamics simulations. We observed the collapse of lipid nanobubbles and the formation of water nanojets. The water nanojets could induce structural changes in membranes. When shock velocities were sufficiently high, the deformed bilayers were hemispherical and water pores were generated. Both the nanojets and the membrane deformations depended on the shock velocity and the initial lipid nanobubble diameter. In the recovery simulations, the bilayers were able to heal themselves, indicating that the bilayer poration was temporary. Besides, compared with the cases of vacuum nanobubbles, the lipid nanobubbles could weaken the effects of shock waves. All this molecular-level information from simulations will be useful for improving the biomedical applications of lipid nanobubbles.