This study conducted 622 single-station microtremor measurements near the boreholes, which were used to generate the hazard map of the soil liquefaction with scale of 1/2500 in Tainan urban area. This study confirmed the consistency of HVSR curves with many measurements within a short time and the long-term periodic measurements. The predominant frequency of the lands in the Tainan urban area is concentrated between 1.0 and 2.0 Hz. The geotechnical properties in each geotechnical zone govern the spatial distribution of the predominant frequency. In addition, we classified the horizontal to vertical spectrum ratio (HVSR) waves as 11 waveforms, and confirmed that the high frequency parts of the HVSR curves, which are higher than the predominant frequency, correlate to the sediment deposit pattern and the depth of the soft soils in the boreholes. This study helps the engineers realize the site effect and highlight the importance of integrating microtremor measurements associating with the high-density borehole data in the seismic disaster mitigations.