In order to study the inherent characteristics and aseismic characteristics of ancient Chinese structure, according to the reconstruction engineering data of the embrasured watchtower on Yong-Ning Gateway of Xi'an City Wall, two finite element models (local and whole models of large timber frame of the embrasured watchtower are built by applying semi-rigid spring element to simulate the mortise-tenon joint, the bracket set and the plinth (that is column base) joint in the real timber structure. The first 10 natural frequencies as well as corresponding vibration modes of the structure are obtained using the method of Block-Lanczos. With full transient analysis, considering time history analysis of two models under the three earthquake excitations of the El-Centro wave, Taft wave and the Lan-Zhou artificial wave, the model displacement and acceleration time history curves were got. By comparing the two model’s basic modeling parameters as well as, the relative errors of the frequencies, the vibration modes, the excitation effects and, the feasibility of using the local model instead of the whole model in the structural analysis were to be discussed one by one. the results show that the local model can stand for the whole model for structural analyzing. Based on the results, the analysis methods and the relevant conclusions could be referenced to study the preservation and the rehabilitation of the ancient Chinese timber structures.