To gain the technical basis for the protection and restoration of the ancient Chinese timber structures, the embrasured watchtower of Yongning Gate of Xi′an City Wall was studied and simulated by the Sap 2000 software. The friction isolation element was applied to simulate the float connection between column and plinth, and the rubber isolator element was applied to simulate tou-kung layer. In addition, the finite element model of the embrasured watchtower was established and consequently a dynamic analysis was carried out by applying the spring element to simulate the mortise-tenon connection. Through the modal contrast analysis to the three models (the rigid connection, hinge, float connection between column foot and plinth), the comparative results showed that the float connection mode could lengthen structures natural periods, and the first three periods were more obvious, which were longer about 72% and 24% compared to rigid connection and hinge of column foot separately. By the response spectrum and the dynamic response time history analyses to the timber structure model, the dynamic magnification factors of each layer were obtained, which showed that the vibration isolation performance of ancient Chinese timber structure mainly manifested in the column foot, tenonmortise connection as well as the p’utso layer. The structural energy dissipation analysis results showed that the majority seismic energy was consumed by the modal damping (average 74.32%) and the tenonmortise connection (average 11.89%).