A semiconductor device structure includes a silicon layer disposed over a first semiconductor die, and a first mask layer disposed over the silicon layer. The semiconductor device structure also includes a second semiconductor die disposed over the first mask layer, and a through silicon via penetrating through the silicon layer and the first mask layer. A bottom surface of the through silicon via is greater than a top surface of the through silicon via, and the top surface of the through silicon via is greater than a cross-section of the through silicon via between and parallel to the top surface and the bottom surface of the through silicon via.