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In this paper, using the finite element software PERFORM3D to establish the finite element analysis model for isolation and seismic frame structure with special-shaped column and rectangular column frame structure, and the overall structure of the moderate and strong elastic and nonlinear earthquake time-history analysis to get the dynamic characteristics, from two aspects of the damping coefficient in horizontal direction and the energy dissipation, investigation structure in earthquake and rare earthquake of superstructure stiffness attenuation. It can be drawn only seismic resistance measures are taken, the special-shaped column structure under rare earthquake stiffness attenuation speed is greater than the rectangular column, if after using base isolation technology, although the special-shaped column stiffness attenuation rate is still greater than the rectangular column, but the two energy dissipation ability.