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Three-dimensional integrated circuit (3D IC) is emerging as an attractive option for overcoming the barriers in interconnect scaling. The majority of the existing 3D IC research is focused on how to take advantage of the performance, power, smaller form-factor, and heterogeneous integration benefits that offered by 3D integration. However, all such advantages ultimately have to translate into cost savings when a design strategy has to be decided: Is 3D integration a cost effective technology for a particular IC design? Consequently, system-level cost analysis at the early design stage is imperative to help the decision making on whether 3D integration should be adopted. In this paper, we study the design estimation method for 3D ICs at the early design stage, and propose a cost analysis model to study the cost implication for 3D ICs, and address the following cost-related problems related to 3D IC design: (1) Do all the benefits of 3D IC design come with a much higher cost? (2) How can 3D integration be achieved in a cost-effective way? (3) Are there any design options to compensate the extra 3D bonding cost? A cost-driven 3D IC design flow is also proposed to guide the design space exploration for 3D ICs toward a cost-effective direction.