A structure and a formation method of a semiconductor device are provided. The semiconductor device includes a semiconductor substrate and a first conductive feature over the semiconductor substrate. The semiconductor device also includes a first dielectric layer over the semiconductor substrate and surrounding the first conductive feature. The semiconductor device further includes a second conductive feature over the first conductive feature, and the second conductive feature extends into the first conductive feature. In addition, the semiconductor device includes a second dielectric layer over the first dielectric layer and surrounding the second conductive feature. The semiconductor device also includes an etch stop layer between the first dielectric layer and the second dielectric layer. The etch stop layer surrounds the first conductive feature, and a bottom surface of the second conductive feature is above the etch stop layer.