In order to scientifically preserve two culturally important imperial stelae, specifically, the north stela and the south stela in Jinling Dabaoen Temple, first the structural performance of these stelae were analyzed by using ANSYS, a type of engineering simulation software. The structural safety issues were investigated under normal conditions and under earthquake conditions. Based on simulation results, a conservation plan is laid out. Adding isolation bearings under the stelae is suggested. The structural performances of the two stelae after adding the isolation bearings were also analyzed by ANSYS. The results showed that the first natural frequency of the north stela (i.e., the imperial stela) was 0.087 times of that of the south stela (lacking the royal stela). Under the earthquake conditions, the imperial stela on the northern site was most likely to be damaged. In the case of the southern stela, the tortoise head was most likely to be damaged first. After installation of bearings, the natural frequencies and the maximum tension and compression stresses of the two stela decreased significantly and became immune to damage even in a seventh degree earthquake. The study provides information about the structural analysis and conservation of stelae.