Gangliosides form high-density nanoclusters in the neuronal cell membrane, and toxic amyloid β protein (Aβ) aggregates are induced by the interaction of Aβ monomers with ganglioside nanoclusters. The shapes of Aβ aggregates, including oligomers and fibrils, were identified via surface topographic studies using atomic force microscopy (AFM) of the planar lipid bilayer. Ganglioside nanocluster-binding molecules are potential candidate inhibitors against Aβ aggregation. We identified artificial peptides that bind to the sugar chains of gangliosides from peptide libraries by biopanning (affinity selection) using phage display technology. AFM and thioflavin T studies indicated that our peptides could bind to Aβ-sensitive ganglioside nanoclusters (ASIGN) and effectively inhibit ganglioside-induced Aβ assemblies. This inhibition suggested that our peptides reduce formation of the ganglioside-bound Aβ (GAβ) complex, which acts as a seed to promote toxic Aβ fibrils. Our results indicate that ganglioside nanocluster-binding peptides (GCBPs) are prospective effective inhibitors against Aβ aggregation in the nervous system.