Embodiments of mechanisms of forming a semiconductor device structure are provided. The semiconductor device structure includes a first semiconductor wafer and a second semiconductor wafer. The first semiconductor wafer includes a first transistor formed in a front-side of the first semiconductor wafer, and the second semiconductor wafer includes a second transistor formed in a front-side of the second semiconductor wafer. A backside of the second semiconductor wafer is bonded to the front-side of the first semiconductor wafer. The semiconductor device structure further includes an interconnect structure formed over the front-side of the second semiconductor wafer, and at least one first through substrate via (TSV) directly contacts a conductive feature of the first semiconductor wafer and the interconnect structure.