A method of manufacturing non-volatile memory devices includes forming a gate insulating layer and a first conductive layer over a semiconductor substrate, etching the first conductive layer and the gate insulating layer to expose part of the semiconductor substrate, forming trenches at a target depth of the semiconductor substrate by repeatedly performing a dry etch process for etching the exposed semiconductor substrate and a cleaning process for removing residues generated in the dry etch process, forming isolation layers within the trenches, forming a dielectric layer on a surface of the entire structure in which the isolation layers are formed, and forming a second conductive layer on the dielectric layer.