In this work, a methodology to extract dynamic multiport compact thermal model from finite element model (FEM) thermal simulations is presented. The proposed methodology is applied to an innovative silicon microthruster. The boundary conditions of the FEM model have been estimated from experimental measurements. The analysis of these transients with the methodology presented delivers a dynamic multiport compact RC model representation of the complete structure. The topology and sizing of the components is provided by a hybrid combination of Sequential Search algorithms together with nonlinear least squares optimization.