The Gyeongju and Pohang earthquakes caused damages to many cultural properties; particularly, stone pagoda structures were significantly damaged among masonry cultural properties. To preserve these structures, it is necessary to understand their dynamic behavior characteristics under earthquakes. Analyses on such areas as deformation, frequency, maximum acceleration, permanent displacement, sliding, and rocking have to be performed. Although many analytical studies have already been conducted, dynamic behavior studies based on experiments are insufficient. Therefore, this study analyzed dynamic behavior characteristics by performing a shaking table experiment on a three-story stone pagoda structure at the Cheollongsa temple site damaged by the Gyeongju earthquake. As a result of the experiment, the displacements of stylobates did not occur significantly, but the tower body parts rotated. In particular, the rotation of the 1F main body stone was relatively larger than that of the other chief body stones because the 1F main body stone is relatively more slender than the other parts. In addition, the decorative top was identified as the component most vulnerable to sliding. This study found that the 1F main body stone is vulnerable to rocking, and the parts located on the upper part are more vulnerable to sliding.