The connected structure refers to the kind of building which is composed of two or more towers connected by the connecting body in a certain height, belonging to the irregular building structure system. According to “Technical Specification for Concrete Structures of Tall Building” (JGJ3-2002), the time-history analysis method should be adopted in the seismic analysis of the connected structure. The structure may have a larger plastic deformation under rare earthquake, so it is difficult to converge when the implicit solution method is used by the conventional finite element software. While the explicit integral technology provided by ABAQUS can solve the nonlinear dynamics problems better, it has a broader application in elastic-plastic dynamic analysis. Taking a specific project as an object, the application of ABAQUS in seismic analysis of connected structures is presented in detail in this paper.