SiP design systems and methods. The system comprises a system partitioning module, a subsystem integration module, a physical design module, and an analysis module. The system partitioning module partitions a target system into subsystem partitions according to partition criteria. The subsystem integration module generates an architecture design and/or a cost estimation for the target system according to the subsystem partitions, at least one SiP platform, and IC geometry data. The physical design module generates a SiP physical design with physical routing for the target system according to the architecture design, the subsystem partitions, the SiP platform, and the IC geometry data. The analysis module performs a performance check within the subsystem partitions based on the SiP physical design and/or simulations of the target system.