One of the objectives of this paper is to understand dynamic soil-structure interaction effects in a ground motion recorded at a seismograph of Nishihara village office during the main shock of the 2016 Kumamoto Earthquake. Another objective is to understand the impact of using the record containing the dynamic soil-structure interaction effects to interpret damages to wooden houses located around the seismograph. First, we conducted sensitivity analyses whose analysis parameters are the characteristics of ground motions and buildings to understand dynamic soil-structure interaction effects on observed records qualitatively. Next, assuming that the ground motion was recorded at the foundation of Nishihara village office, we estimated the ground motions on the free-field by inverse analyses using the dynamic interaction model of Nishihara village office. Finally, simulation analyses of two-story wooden houses were conducted using the estimated ground motions on the free-field.