Random vibration responses of two layer stacked packaging unit in different levels of vibrations and different constraints were experimentally investigated. The finite element method was used to analyze the response of two layer stacked packaging units in the fixed constraint. The results showed that the product vibration in upper layer was mainly controlled by the first resonant frequency, and the product vibration in lower layer was controlled together by the first and second resonant frequencies. The acceleration response of product was large in the area of resonant frequencies, and small in the area of non-resonant frequencies. The power spectrum of product acceleration response was mainly the resonance response spectrum of product. The resonance frequencies and acceleration PSDs of product obtained from the finite element method were in agreement with the experimental ones, which indicated that the finite element method provided an effective tool for the analysis of stacked packaging units in random vibration.