A semiconductor device includes a first substrate, a through substrate via, a second substrate, and a bonding structure. The first substrate includes a first dielectric material, and the first dielectric material includes a first conductive pad embedded therein. The through substrate via is formed in the first substrate. The second substrate includes a second dielectric material, the second dielectric material includes a second conductive pad embedded therein, the first dielectric material is different from the second dielectric material, the second conductive pad has a first height, the second dielectric material has a second height, and the first height is less than the second height. The bonding structure is formed between the first substrate and the second substrate, wherein the bonding structure includes the first conductive pad bonded to the second conductive pad and the first dielectric material bonded to the second dielectric material.