A semiconductor device structure is provided. The semiconductor device structure includes a substrate. The semiconductor device structure also includes a first isolation structure partially embedded in the substrate. The first isolation structure has a first upper surface with a first recess. The semiconductor device structure further includes a second isolation structure partially embedded in the substrate. In addition, the semiconductor device structure includes a first gate over the substrate and between the first isolation structure and the second isolation structure. The first gate extends onto the first upper surface to cover the first recess. The semiconductor device structure includes a second gate over the first gate.