The purpose of this study is to clarify the seismic performance of piled raft foundations with ground improvement based on seismic observation records. The monitored building, which is a twelve-story base-isolated structure, is located on loose silty sand underlain by soft cohesive soil in Tokyo, Japan. On March 11, 2011, when the 2011 off the Pacific Coast of Tohoku Earthquake struck the building site, the seismic response of the soil-foundation-structure system was successfully recorded during the earthquake. This paper presents a simulation analysis of the seismic behavior of the building during the earthquake using a detailed three dimensional finite-element model. The simulation agrees well with the observed peak acceleration reduction of the superstructure created by the base-isolation system, with the bending moments on the piles increased due to large ground deformation.