A method for manufacturing an isolation structure integrated with semiconductor device includes following steps. A substrate is provided. A plurality of trenched gates is formed in the substrate. A first insulating layer and a second insulating layer are sequentially deposited on the substrate. A first etching process is performed to remove portions of the second insulating layer to expose portions of the first insulating layer. A second etching process is then performed to remove the exposed second insulating layer to expose the trenched gates and to define at least an active region.