Site effects inducing the amplification of earthquake ground motion are strongly influenced by the local geologic conditions such as soil thickness and stiffness. Most of major cities in the world are located across wide area where there are various surface topographies and corresponding subsurface geotechnical conditions. To prepare earthquake-induced structural damages and corresponding casualties in an urban area, hence, the spatial prediction of geotechnical information in the entire region is not only important but fundamental. In this study, to predict reliably spatial geotechnical information based on restricted number of boring data, a procedural methodology is introduced and applied into GIS tool. Particularly, an inland metropolitan city, Daegu, in Korea, was selected for implementing an integrated GIS-based geotechnical information system. Based on the various data combined over the area of interest, geotechnical layers information was reliably predicted in the entire region of Daegu with three-dimensional feature. For practical application of geotechnical information to assessing the site effects in the target urban area, seismic zoning maps of bedrock depth and site period were created and presented as regional basic information on seismic disasters. Spatial distribution on seismic structural vulnerability potential in the area of interest was intuitively examined from the seismic zoning maps. Furthermore, seismic zonations were also performed to determine the site amplification coefficients for seismic design and seismic performance evaluation of structures in the Daegu area.