Earthquakes occur frequently in Taiwan as it is located at the junction of the Eurasian continental plate and the Philippine Sea plate. Hence, for the maintenance and utilization of historical buildings in Taiwan, ensuring their seismic performance is an important issue. After the occurrence of the Meinong earthquake on Feb 6th, 2016, which triggered strong shakings greater than intensity level 7, according to the Cultural Bureau of Tainan City, more than half of the historical building cases damaged by the earthquake were traditional masonry temples. Considering the large number of traditional temples exsisting all over Taiwan, and their structural similarity, once another strong earthquake occurs, traditional temples may subject to similar high damage ratio. In view of this, traditional masonry temples in Tainan subject to seismic intensity level greater than 5 are considered in this study. First, their damage pattern in the Meinong earthquake and the relationship with structural characteristics are investigated, such as wall ratio, load of unit area, and base shear coefficient. From the analysis resalts, for the in-plane direction of side walls, damage of masonry walls may occur, when the wall ratio is less than 0.08, and the load of unit area is greater than 5000kgf/m2. Based on the calculation of the shear strength of wall, it can be identified that damage occurs when the seismic inertia force attains approximately 6.3% and 6.1% of the yield and ultimate shear strength of the wall, respectively. In addition, this study conducted ambient vibration measurement to obtain the natural vibration frequency of the temple. The regression between measured natural frequency and geometric parameter of the temple showed good relation as the R-squared value was greater than 0.8. The natural frequency of the surveyed temples ranged 10~15 Hz and 5~8 Hz for the in-plane and out-of-plane direction, respectively. Due to the structural similarity of masonry temples, the results obtained in this study can be applied to temples across the country, in order to prevent damage in strong earthquakes and to maintain the integrity of historical buildings in advance.