The Peinan archaeological site is the largest prehistoric village in Taiwan. Only small-scale pits are allowed for research purposes because the Peinan site is protected by the Cultural Heritage Preservation Act. Careful selection of the pit locations is crucial for future archaeological research at this site. In this study, a ground-penetrating radar (GPR) survey was applied near the stone pillar to understand the GPR signatures of the subsurface remains. Seven GPR signatures were categorized based on the radar characters shown on the GPR image. A detailed GPR survey with dense parallel survey lines was subsequently conducted in the area of northern extent of the onsite exhibition to map the subsurface ancient buildings. The results were verified by two test pits, which indicate that the distribution of the subsurface building structures can be well recognized from GPR depth slices. It will be very helpful for setting proper pits priorities for future archaeological research, and for making proper design of the new onsite exhibition.