Because shaking modes of super high-rise buildings are very complicated, it is not enough to perform health-monitoring only for the whole structures. We try to extract story-by-story shear-wave velocities applying the deconvolution method to microtremor records measured at super high-rise buildings. The shear-wave propagation (including reflection, transmission, and interferometry at the boundary of stories) extracted from microtremor records are compared with those simulated ones using 2-D frame models with different mass-and-rigidity distributions which lead to different shaking modes. Story-by-story shear-wave velocities can be extracted from buildings whose shaking modes of all the stories are mainly shear modes. However, the shear-wave velocities of the buildings cannot be extracted successfully, if the stories are shaking in pure bending mode, because no inter-story shear deformation happened, the apparent shear-rigidities of these stories can be seen as infinite, which lead shear-wave travel times to zero.