A method of fabricating a nonvolatile memory device with a three-dimensional structure includes alternately stacking first and second material layers in two or more layers on a semiconductor substrate, forming trenches penetrating the stacked first and second material layers by performing a first etching process, and removing the second material layers exposed in the trenches by performing a second etching process. The first and second material layers are formed of materials that have the same main component but have different impurity contents, respectively.