During the 2011 off the Pacific coast of Tohoku Earthquake, Nagamachi Viaducts on the Tohoku Shinkansen Line, Sendai City, Miyagi Prefecture, Japan, suffered significant damage. In order to analyze the damage mechanism, it is important to evaluate strong ground motions at the viaduct sites with high accuracy, taking into account site effects. In this study, seismic waveforms along the viaduct were estimated based on the SPGA model considering empirical site amplification and phase effects. Using the actual damage data and detailed distribution of the estimated ground motion, this study conducts the statistical analysis on the relationship between the damage ratio and several indices of the ground motion to construct fragility curves. The estimated ground motions and fragility curves will be useful in the detailed study of the damage mechanism.