During the 2007 Noto-hanto Earthquake, the town of Anamizu experienced severe damage, though the town is located about 20 km away from the epicenter. More than 70 of wooden houses were completely collapsed in the area of 500 m square and the damage was remarkably concentrated in the zone of 100 m square. We measured micro-tremor at more than fifty locations and found that the area with collapsed houses has predominant frequency between 1.1 Hz and 3.0 Hz and the concentrated damage zone has about 2.0 Hz. Two layered irregular subsurface model was constructed by simulating H/V spectrum peak frequencies with frequency dependence of the particle motion of Rayleigh wave fundamental mode. The concentrated damage zone seems to lay on thick soft layer of 12 m to 15 m surrounded by shallower bedrock with thinner surface layers; the zone seems to locate at the mouth of a bay of about 200 m wide. The two dimensional FEM model with Ricker wave incidence reveals the constructive interference of reverberation and the Rayleigh waves. The ground motion during the main shock was evaluated by the 2-D FEM equivalent linear analysis with simulated incident waves and soil non-linearity of surface layers, which reveals about 10 % increase of response spectrum around 1 Hz.