Since accurate thermal analysis is essential for the design and thermal management of System-in-Package (SiP). This paper proposes a transient thermal analysis of the System-in-Package technology based on four chips, in order to investigate the effect of the underlying layers on the thermal model. The finite element method (FEM) using the COMSOL Multiphysics® tool is proposed to achieve this objective. The temperature variation in the numerical simulation shows that the underlying layers are very important in decreasing the maximum temperature value of the SiP. Moreover, in terms of thermal conduction performance, and thermal management of the packaging system, this transient thermal analysis achieves high reliability and resolution when the maximum temperature in the chips is reduced by 16 °C.