The ever increasing die area of Chip Multiprocessors (CMPs) affects manufacturing yield, resulting in higher manufacture cost. Meanwhile, network-on-chip (NoC) has emerged as a promising and scalable solution for interconnecting the cores in CMPs, however it consumes significant portion of the total die area. In this paper, we propose to decouple the interconnect fabric from computing and storage layers, forming a separate layer called Interconnect Service Layer (ISL), in the context of three-dimensional (3D) chip integration. Such decoupling helps reduce the die area for each layer in 3D stacking. ISL itself can integrate multiple superimposed interconnect topologies. More importantly, ISL can be designed, manufactured, and tested as a separate Intellectual Property (IP) component, which supports multiple designs in the computing and storage layers. The resulting methodology also helps support different manufacturing volume in each die of 3D to reduce the overall manufacturing cost. We demonstrate the proposed methodology with an ISL design example and compare to its 2D and 3D counterparts without ISL support. The results show that 3D design with ISL not only provides significant cost reduction, but also achieves power-performance improvement thanks to the efficient usage of ISL.