A method for fabricating memory device is provided. The method comprises forming a cell structure on a substrate, wherein the cell structure comprises a first gate structure and a second gate structure disposed on a substrate and an insulating layer in contact between the first gate structure and the second gate structure, wherein the first gate structure and the second gate structure are planarized and the first gate structure is for storing charges. Further, the first gate structure and the second gate structure are patterned to have a shallow indent above the insulating layer. An isolation structure is formed in the shallow indent to have a shallow indent isolation.