Three-dimensional integration circuit (3D IC) offers significant benefits in terms of performance and cost. Existing research in through-silicon via (TSV)-based 3D IC partitioning has focused on minimizing the number of TSVs to reduce costs. Partitioning methods based on heterogeneous integration have emerged as viable approaches for cost optimization. Leveraging mature processes to manufacture not timing-critical blocks can yield cost benefits. Nevertheless, none of the previous 3D partitioning work has focused on reducing the overall cost, including both design and manufacturing costs, for heterogeneous 3D integration. Moreover, throughput constraints have not been considered. This article presents a cost-aware integer linear programming-based formulation and a heuristic algorithm that partition the functional blocks in the design into different technological groups. Each group of functional blocks will be implemented using a particular process technology, and then integrated into a 3D IC. Our results show that 3D heterogeneous integration chip implementation can reduce overall cost while satisfying various timing constraints.