For the analysis of vibrational energy density and intensity of partitioned complex system structures in medium-to-high frequency ranges, A software based on the Power Flow Analysis(PFA) has been developed for the plate elements. The flexural, longitudinal and shear waves in plates are formulated and the joint element equations for multi-coupled plates are fully developed. Also, the wave transmission approach has been introduced to cover the energy transmission and reflection at the joint plate elements. To confirm the validity of the developed PFA software, the submarine-shaped complex structures are used for the analysis of vibration intensity and energy density.