Spectrum characteristics of different types of seismic waves and dynamic response characteristics of super high-rise building structures under long-period ground motions were comparatively analyzed. First, the ground response wave (named LS-R wave) of a soft soil site with deep deposit, taking long-period bedrock seismic record as input, was calculated by wave propagation method. After that, a TOMAKOMAI station long-period seismic record from the Tokachi-Oki earthquake and conventional El-Centro wave were also chosen. Spectrum characteristics of these waves were analyzed and compared. Then, a series of shaking table tests were performed on a 1:50 scale super high-rise structural model under these seismic waves. Furthermore, numerical simulation of the prototype structure under these excitations was conducted, and structure damages under different intensive ground motions were discussed. The results show that: 1) Spectrum characteristics of ground response wave are significantly influenced by soft soil site with deep deposit, and the predominant period has an increasing trend. 2) The maximum acceleration amplification factor of the structure under the TOM wave is two times that under the El-Centro wave; while the maximum displacement response of the structure under the TOM wave is 4.4 times that under the El-Centro wave. Long-period ground motions show greater influences on displacement responses than acceleration responses for super high-rise building structures. 3) Most inelastic damage occurs at the upper 1/3 part of the super high-rise building when subjected to long-period ground motions. Spectrum characteristics of different types of seismic waves and dynamic response characteristics of super high-rise building structures under long-period ground motions were comparatively analyzed. First, the ground response wave (named LS-R wave) of a soft soil site with deep deposit , taking long-period bedrock seismic record as input, was calculated by wave propagation method. After that, a TOMAKOMAI station long-period seismic record from the Tokachi-Oki earthquake and conventional El-Centro wave were also chosen. Spectrum characteristics of these waves were, analyzed and compared. Then, a series of shaking table tests were performed on a 1:50 scale super high-rise structural model under these excitions were conducted, and structural damages different intensive ground motions were discussed. The results show that: 1) Spectrum characteristics of ground response wave are significantly influen ced by soft soil site with deep deposit, and the predominant period has an increasing trend. 2) The maximum acceleration amplification factor of the structure under the TOM wave is two times that under the El-Centro wave; while the maximum displacement response of the structure under the TOM wave is 4.4 times that under the El-Centro wave. Long-period ground motions show greater influences on displacement responses than acceleration responses for super high-rise building structures. 3) Most inelastic damage at the upper 1/3 part of the super high-rise building when subjected to long-period ground motions.