A device includes an interposer including a substrate having a top surface and a bottom surface. A plurality of through-substrate vias (TSVs) penetrates through the substrate. The plurality of TSVs includes a first TSV having a first length and a first horizontal dimension, and a second TSV having a second length different from the first length, and a second horizontal dimension different from the first horizontal dimension. An interconnect structure is formed overlying the top surface of the substrate and electrically coupled to the plurality of TSVs. The invention further provides the TSVs with different sizes in interposers for bonding dies.