We have chosen the GPR method for investigating the inner structure of a stone pagoda in a non-destructive way. The selection of a suitable source frequency of the GPR antenna is the key because the main frequency of its pulse controls the resolution and the depth of the investigation. Through theoretical consideration and numerical simulation, we found that 500 to 800 MHz is suitable for a field model with a foundation part of 3 to 4 m. To image the inner structure we selected 3-D Kirchhoff prestack depth migration technique used in seismic processing. We have used the modified migration algorithm for the source and receiver configurations of common offset GPR data. To verify the scheme, we calculated the synthetic data using the 3-D FDTD algorithm and applied the migration technique to it. Through these experiments, we confirmed that the 3-D Kirchhoff prestack depth migration technique is a very powerful tool to image the inside of a stone pagoda with high resolution. We have also applied the technique to the field data of the foundation of a five-story stone pagoda at Jeongnim temple site in Buyeo City, Korea. Based on the 3-D migrated images, we inferred that the structure of the foundation of this pagoda seemed to be preserved quite well and the thickness of the outer wall was about 0.5 m.