In accordance with some embodiments, a semiconductor device structure is provided. The semiconductor device structure includes a substrate, and the substrate has a cell region and a logic region. The semiconductor device structure also includes an isolation feature formed in the substrate and a first gate stack structure formed on the isolation feature and at the cell region. The semiconductor device structure further includes a second gate stack structure formed on the isolation feature and at the cell region, and the first gate stack structure is adjacent to the second gate stack structure. The isolation feature between the first gate stack structure and the second gate stack structure has a substantially planar topography.