A method of forming a shallow trench isolation structure is disclosed. Hard mask patterns are formed on a substrate. A portion of the substrate is removed, using the hard mask patterns as a mask, to form first trenches in the substrate, wherein a fin is disposed between the neighboring first trenches. A filling layer is formed in the first trenches. A patterned mask layer is formed on the filling layer. A portion of the filling layer and a portion of the fins are removed, using the patterned mask layer as a mask, to form second trenches in the substrate. A first insulating layer is formed on the substrate filling in the second trenches.