In design of super high-rise structure, the ground motion intensity index guides the seismic design of the structure and is very important for safety of the structure,but there is no unified conclusion on the ground motion intensity index of super high-rise mixed structure. Therefore, it is of great significance to study the ground motion intensity index of the super high-rise structure. Based on the review of the current research status of the effectiveness of seismic intensity index in the incremental dynamic analysis of building structures, this article proposes a seismic intensity index a%, which is suitable for the incremental dynamic analysis of super high-rise building structure. The ground motion intensity index S_a% is the geometric average of the spectral acceleration corresponding to the natural vibration period of a% mode mass participation coefficient before considering the translational direction of the structure. In order to verify the effectiveness of the seismic intensity index S_a%, PERFORM-3D elastoplastic analysis software was used to establish a nonlinear model of an actual super high-rise building and perform incremental dynamic analysis. Based on the discrete analysis of θ_max and V_max results of various ground motion intensity indexes, it is concluded that S_a% of ground motion intensity index proposed in this paper can effectively reduce the discreteness of θ_max and V_max when applied to incremental dynamic analysis of super-high-rise structures, which improves the validity of calculated data and provides reference for the application of actual super high-rise structures.