Ancient timber buildings are precious treasure of Chinese nation.However, some of them have suffered different types and degrees of damage after hundreds of years of service, which reduces the safety performance of structures. In this paper, the Tongdao Hall in the Imperial Palace at Beijing is chosen as the research object. Through on-site investigation and damage analysis, the typical damage types, characteristics, influences, quantity and distribution law of structural column frame layer, Dougong layer and beam frame layer are obtained. The causes of its damage are summarized and the protection suggestions are proposed. The results show that the types of structural damage mainly include component cracking, decay, missing, inclination, separation, and pulling-out of tenon joint, etc. Especially, the damage at the column frame layer is the most complex and serious. The reasons for structural damage can be summarized as material degradation and timber defects, biological erosion and variation of natural environment, long-term complex loading effect and irrationality of repair. Establishing structural health monitoring system, strengthening biological disease prevention and control, and promoting the basic research onmechanical performance of timber structures are essential for protection and repair of ancient buildings.