In the two middle-scale atlases made by Japanese colonial government of Taiwan in the early twentieth century, there are abundant sets of spatial information. Through GIS technique, these sets of information can be systematically extracted and integrated into numerous historical thematic maps, which provide concrete historical spatial reference and might fertilize various fields of humanistic studies on Taiwan history. By the comparison of these atlases, which had a panoptic enterprise revealed in other topographical maps as well, we could spatially represent and reinterpret the early twentieth-century transformation, especially the deployed modern institutions and facilities under the Japanese colonial rule. Furthermore, this article engages a reflection of colonial mapping, beyond the way argued by cartographic historians who cannot use GIS. Finally, take this reflexivity into GIS on historical study itself.