Thousands of wooden houses were destroyed by the 2016 Kumamoto Earthquake. A seismic damage prediction function for wooden houses taking into consideration the consecutive strong earthquake motions, the amplification effect of ground surface layer, and the rupture propagation effect of seismic fault was proposed in this paper. Relationship between three ground characteristics above mentioned and the seismic damage for wooden house in the 2016 Kumamoto earthquake was analytically investigated by 3-D collapsing process analysis. The maximum drift angle was evaluated in this collapsing analysis of two-story wooden house.