An isolation oxide film whose upper surface is higher than a surface of a substrate is formed in the substrate. A silicon oxide film is formed on the substrate between the isolation oxide films. A self-aligned polysilicon film is formed on the silicon oxide film between the isolation oxide films. After forming a resist pattern covering the peripheral circuitry, the isolation oxide films in the memory cell are etched by a predetermined thickness. An ONO film is formed on the entire surface of the substrate, a second resist pattern covering the memory cell is formed. Then, the ONO film, the polysilicon film 8 and the silicon oxide film 7 are removed from the peripheral circuitry.