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This paper presents a novel design flow for three-dimensional (3D) heterogeneous system prototyping platform, namely, MorPACK (morphing package). The 3D-stacking technique makes the MorPACK platform with heterogeneous integration capabilities through connection modules and circuit modules. Based on system partition and tri-state interface connecting, the MorPACK system can be efficiently extended by system bus interfaces and can improve the functions by only updating the bare die/module. In addition, the total silicon prototyping cost of heterogeneous SoC projects can be greatly reduced by sharing the MorPACK common system platform. To demonstrate the effectiveness of the proposed platform, six SoC projects are implemented. The results show that there are 79.13% fabrication cost reduced by the MorPACK platform in TSMC 90nm CMOS. Besides, around 60% performance improvement of operation frequency can be benefited.