System in Package (SiP) is widely used to miniaturize electronic systems and increase their level of integration. Since reliability and lifetime estimation depend critically on accuracy of thermal models and temperature of inter-layers that constitute the SiP, a Foster based model is proposed to achieve this purpose. In this model, heat transfer between layers of the system and thermal coupling between dies in vertical and horizontal plane are accurately taken into account. As a proof of concept, detailed 3D modeling of a multichip heterogeneous module is performed with Simulink. This model can be used for real-time temperature prediction. The accuracy of predicted junction and inter-layer temperatures are confirmed by Finite Element Method (FEM) analysis.