A method of manufacturing a nonvolatile memory device having a three-dimensional memory device includes alternately stacking a plurality of first and second material layers having a different etching selectivity on a semiconductor substrate; forming an opening penetrating the plurality of first and second material layers; removing the first material layers exposed by the opening to form extended portions extending in a direction perpendicular to the semiconductor substrate from the opening; conformally forming a charge storage layer along a surface of the opening and the extended portions; and removing the charge storage layer formed on sidewalls of the second material layers to locally form the charge storage layer patterns in the extended portions.