In Chinese Design Codes, for super high-rise buildings with complex structural distribution, which are regarded as code-exceeding buildings, elasto-plastic time history analysis is needed to validate the requirement of "no collapse under rare earthquake". In this paper, a 117-story super high-rise building is discussed. It has a height of 597 m and a height-width ratio of 9.5, which have both exceeded the limitations stipulated by the Chinese Design Codes. Mega columns adopted in this structure have cross section area of about $45m^2$ at the bottom, which is infrequent in practical projects. NosaCAD and Perform-3D, both widely used in nonlinear analyses, were chosen in this study, with which two model were established and analyzed, respectively. Elasto-plastic time history analysis was conducted to look into its seismic behavior, emphasizing on the stress state and deformation abilities under intensive seismic excitation.From the comparisons on the results under rare earthquake obtained from NosaCAD and Perform-3D, the overall responses such as roof displacement, inter story drift, base shear and damage pattern of the whole structure from each software show agreement to an extent. Besides, the deformation of the structure is below the limitation of the Chinese Codes, the time sequence and distribution of damages on core tubes are reasonable, and can dissipate certain inputted energy, which indicates that the structure can meet the requirement of "no collapse under rare earthquake".