A semiconductor device includes a first substrate having a first surface and a second surface opposite to the first surface, a shallow trench isolation in the first substrate, the shallow trench isolation having a first depth, the first depth being a distance from a bottom of the shallow trench isolation to the first surface of the first substrate, a transistor on the first surface of the first substrate, a first dielectric cap layer covering the first surface of the first substrate, a first interconnect structure on the first dielectric cap layer, a carrier substrate bonded to the first substrate through the first dielectric cap layer, a second dielectric cap layer on the second surface of the first substrate; and a through silicon via extending through the second dielectric cap layer, the shallow trench isolation, and the first dielectric cap layer, and connected to the first interconnect structure.