This study uses Ordinary Kriging (OK), Sequential Gaussian Simulation (SGS) and Simulated Annealing Simulation (SAS) to relocate the completely heterotopic dataset from the locations of the Standardized Satellite Oriented Control Point System (SSOCPS) stations to the Groundwater Monitoring Networks (GMNS) stations and factorial kriging to analyze and map relationships among seven variables, including the hydraulic conductivities of three aquifers, the vertical displacements of the ground and groundwater level changes in the wells of three aquifers, and also to delineate the anomalies of multi-scale spatial variation of hydrogeological properties associated with the ChiChi earthquake, measuring 7.3 on the Richter scale, in the ChouShui River alluvial fan in Taiwan. In this study, the anomalies of spatial variation of hydrogeological properties associated with the earthquake are illustrated at micro, local and regional scales of 9, 12 and 36 km, respectively. In the study area, regionalization components associated with variation at local and regional scales are obtained and mapped by factorial kriging. Factorial Kriging Analysis (FKA) also demonstrated that the main effects of the ChiChi earthquake on the spatial variations of groundwater hydrological changes include porous media compression at micro scale, hydrogeological heterogeneousness of the sediments within the aquifer at local scale and the cyclic loading of deviatoric stress at regional scale. Finally, maps of spatial variations of regional components fully depicted all of the anomalies of spatial variation of hydrogeological changes due to the ChiChi earthquake and can be used to identify, confirm and monitor the hydrogeological properties in this study area.