Dynamic characteristics and seismic response for unequal height double-tower structure models were analyzed by finite element software. The effort of the connecting beam location changes to the structural vibration period, the maximum displacement on top and the maximum shear force at bottom were analyzed and compared. The results indicate that horizontal displacement under the seismic waves in x direction is larger than the displacement under seismic waves in y direction. When the locations of the connecting body vary, the influence to structural vibration period is different as vibration modes change. The effort to the maximum shear force of the structure at bottom under the seismic waves in x direction is larger than the displacement in y direction. The above results provide references for design and further studying.