The compound power-split mechanism (CPSM) has a compact structure and high power density, and is widely used in new energy vehicles, aerospace, and military industries. However, owing to the large scale of CPSM schemes composed of two PGSs, the optimization time is too long, and the design process cannot realize rapid design and optimization by using a computer. To realize the rapid computer solution and analysis of the kinematic characteristics of CPSM, the configuration synthesis method based on the structural matrix is constructed by not only considering the internal interconnection relationship of the two planetary gear sets (PGS) in CPSM but the powertrain distribution mode is proposed in this paper. First, the unified lever model is constructed by making the length of the shared lever between the two PGSs equal, whereas the remaining lever length is multiplied by the relevant multiple. Second, to establish a synthetic matrix, the influence of the powertrain distribution was also considered. Third, the normalization matrix is constructed by comprehensively considering the unified lever model and the synthetic matrix. Finally, the synthetic, normalization, and length matrices are multiplied from left to right to construct the system structural matrix, which can describe the unique structural characteristics of any CPSM configuration scheme to ensure that all isomorphisms can be identified. The results show that the configuration synthesis method is 215 times more efficient than the traditional method in searching for high-performance CPSM configurations, and can also be applied to complex CPSM and differential gear train analysis.