This paper introduces the research status of efficiency of seismic intensity index in the incremental dynamic analysis of building structure, and puts forward the seismic intensity index `Sa%, which is suitable for the incremental dynamic analysis of super high-rise building structure, on the basis of the existing research results. In a real superiors as an example, use PERFORM-3D elastic-plastic analysis software to establish a nonlinear model and incremental dynamic analysis, based on the results of a plurality of seismic intensity indicators for discrete analysis of the results, it is verified that the proposed `S90% will effectively reduce the dispersion of calculated data when used in the incremental dynamic analysis of super-high-rise structures.