We performed microtremor array survey in the Iwaki City Hall in Fukushima prefecture, Japan in order to estimate underground structure beneath the site and to understand the effectiveness, limitations, and advantages of surface-wave array measurements as a tool for seismic microzonation and earthquake disaster mitigation. Two methods were applied to microtremor and surface wave data: the spatial auto-correlation (SPAC) method and the multi-channel analysis of surface waves (MASW) method with common mid-point cross correlation (CMPCC) analysis. The SPAC method performed well in relatively low frequency range (0-5Hz) that covers deep shear wave velocity (Vs) structure and the results show that the engineering bedrock (Vs > 400m/s) depths are deeper than 40 m. The MASW method has advantages in higher frequency range (5-20Hz) that covers lateral variations of shallow underground structure and the results show that the subsurface soft layer (Vs < 150m/s) varies between 15-40m. These results indicate that the soft sediment layers are several tens of meters in thickness and characteristics of the estimated Vs structure were comparable to those from the reference borehole data, indicating the soft sediment bottom declines more deeply from east to west. The study has shown that the combination of the SPAC and the MASW methods is an effective tool for seismic microzonation with more stable resolution.