In a method for manufacturing a dual shallow trench isolation structure, a substrate is provided, and a mask layer is formed on the substrate. The mask layer is patterned by using a photomask to form at least one first hole and at least one second hole in the mask layer, in which a depth of the at least one first hole is different from a depth of the at least one second hole. The mask layer and the substrate are etched to form at least one first trench having a first depth and at least one second trench having a second depth, in which the first depth is different from the second depth. The remaining mask layer is removed. A first isolation layer and A second isolation layer are respectively formed in the at least one first trench and the at least one second trench.