A method includes forming an interconnect structure over a semiconductor substrate. The interconnect structure includes a plurality of dielectric layers, and the interconnect structure and the semiconductor substrate are in a wafer. A plurality of metal pads are formed over the interconnect structure. A plurality of through-holes are formed to penetrate through the wafer. The plurality of through-holes include top portions penetrating through the interconnect structure, and middle portions underlying and joining to the top portions. The middle portions are wider than respective ones of the top portions. A metal layer is formed to electrically connect to the plurality of metal pads. The metal layer extends into the top portions of the plurality of through-holes.