To study the seismic performance of a super high-rise building, a shaking table test with a geometrical scale of 1/35 was carried out. Part of frames in the tower structure of the building are supported by two concrete-filled steel tubular (CFST) mega frame columns with duplex-story height, which are not connected to the first 6 floors. The inclined CFST column transfer structure is arranged on the 7th to 11th floors. Through experiments, failure modes, natural vibration period, story drift, and torsional responses of the structural model were studied first. Then, a numerical analysis of the elastic-plastic seismic response of the original structure was carried out via PERFORM-3D software. Results show that torsion effects were significant because of the asymmetric plane arrangement and the inadequate torsional stiffness of the tower. When the actual peak acceleration on the shake table surface was close to the value of the rare earthquake condition (i.e., 470 cm/s2), the torsional failure occurred in the tower. In this condition, except for very few stories, the story-drift angle of each floor was still smaller the limit value 1/100 of the elastic-plastic story-drift angle. Under all load conditions, the strains of CFST frame columns and inclined ones of the transfer areas stayed elastic. The analysis results are in good agreement with those of experiments.