The system LSI has been improved its values by increasing its circuit scaling and technology scaling based on Moore's law. However, semiconductor devices are expected to face physical and economical miniaturization limits in the near future, and traditional technology scaling based on the Moore's law is going to fail. Therefore, 3D technology, like 3D-SiP (System-in-Package), has been realized rapidly as a key to break through these limits. However, by increasing circuit scaling and evaluation point such as heat caused by shift to 3D structure, design quality is reduced, because it becomes difficult to define and visualize whole system. In this paper, using SysML (System Modeling Language), which is generally used for defining systems, we visualize whole system and optimize 3D-SiP system.