Advances in integrated circuit and package technologies, such as the increase of the number of metal layers and 3-D stacking technique, have paved the way for faster speed and higher performance in today's electronic products. However, whether the high-speed systems preserve signal integrity has become a crucial question for system designers. In this work, we introduce a systematic numerical simulation method for 3-D full package simulation. A non-conformal finite element domain decomposition method with second order transmission condition is proposed to iterative the matrix equation solution. Numerical results verify the analysis and demonstrate the effectiveness of the proposed method on a real-life 3-D full package signal integrity analysis.