Building upon our previous studies on interactions of amphiphilic Janus nanoparticles with glass-supported lipid bilayers, we study here how these Janus nanoparticles perturb the structural integrity and induce shape instabilities of membranes of giant unilamellar vesicles (GUVs). We show that 100 nm amphiphilic Janus nanoparticles disrupt GUV membranes at a threshold particle concentration similar to that in supported lipid bilayers, but cause drastically different membrane deformations, including membrane wrinkling, protrusion, poration, and even collapse of entire vesicles. By combining experiments with molecular simulations, we reveal how Janus nanoparticles alter local membrane curvature and collectively compress the membrane to induce shape transformation of vesicles. Our study demonstrates that amphiphilic Janus nanoparticles disrupt vesicle membranes differently and more effectively than uniform amphiphilic particles.