The configuration of nine-speed automatic transmission (AT) is one of the most important factors to determine its performance, and the pursuit of a better configuration of AT has always been the research focus. This paper proposes a new structural decomposition method, based on which the configuration synthesis of nine-speed AT with a cut-link is conducted by the combination of two independent planetary gear trains (PGT). Firstly, two different decomposition types are introduced, and the structure of nine-speed AT with four planetary gear sets (PGSs) and two degrees of freedom (DOF) is divided into two substructures with one-DOF. Secondly, all the topological graphs of substructures in the two decomposition types are obtained by screening in our atlas database. Thirdly, the layouts of shifting elements (SEs) are analyzed based on the lever method, and all the possible layouts of SEs are obtained. Finally, the substructures are combined according to the layouts of SEs to synthesize the configurations of nine-speed AT. As a result, 168 different configurations of AT are obtained including some classical and new configurations. Furthermore, the method can be extended to the synthesis of other multi-speed ATs.