A method for fabricating intra-device isolation structure is provided, including providing a semiconductor substrate with a mask layer formed thereover. A plurality of first trenches is formed in the semiconductor substrate and the mask layer. A first insulating layer is formed in the first trenches. The mask layer is partially removed to expose a portion of the first insulating layer in the first trenches. A protection spacer is formed on a sidewall surface of the portion of the first insulating layer exposed by the mask layer to partially expose a portion of the mask layer between the first insulating layer. An etching process is performed to the mask layer exposed by the protection spacer and the semiconductor substrate thereunder, and a plurality of second trenches is formed in the semiconductor substrate and the mask layer. A second insulating layer is formed in the second trenches. The protection spacer, the mask layer, the first insulating layer and the second insulating layer over a top surface of the semiconductor substrate are then removed.