In general, the stone pagoda structures with discontinuous surfaces are vulnerable to lateral forces and are severely damaged by earthquakes. After the Gyeongju earthquake in 2016 and the Pohang earthquake in 2017, the earthquakes damaged numerous stone pagoda structures due to slippage, rotation and the separation of stacked stone. To evaluate seismic resistance of masonry stone pagoda structure, we analyzed the seismic behavior of stone pagoda structure using shaking table test. Shaking frequency, permanent displacement, maximum acceleration, rocking, and sliding were assessed. Responses to simulations of the Bingol, Gyeongju, and Pohang earthquakes based on Korean seismic design standard (KDS 41 17 00) were analyzed for return periods of 1,000 and 2,400 years. We found that the type of stylobate affected the seismic resistance of stone pagoda structure. When the stylobates were stiff, seismic energy was transferred from lower to upper regions of the stone pagoda, which mainly resulted in deformation of the upper region. When the stylobates were weak, earthquake energy was absorbed in the lower regions; this was associated with large stylobate deformations. The lower part of tower body was mainly affected by rocking, because the structural members were slender. The higher part of the stone pagoda was mainly affected by sliding, because the load and contact area decreased with height.