A semiconductor device structure is provided. The semiconductor device structure includes a semiconductor substrate having a top surface, a source region, and a drain region. The semiconductor device structure includes a gate structure over the top surface and extending into the semiconductor substrate. The gate structure in the semiconductor substrate is between the source region and the drain region and separates the source region from the drain region. The semiconductor device structure includes an isolation structure in the semiconductor substrate and surrounding the source region, the drain region, and the gate structure in the semiconductor substrate.