Ancient timber buildings are the precious treasure of Chinese nationality, but they 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 is chosen as object. Through on-site investigation and damage analysis, the typical damage types, characteristics, influences, quantity and distribution of structural column frame layer, Dougong layer and beam frame layer are obtained. The damage reasons 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. The damage condition of column frame layer is the most complex and serious. The reasons of structural damage can be summarized as material degradation and timber defects, biological erosion and variation of natural environment, long-term complex load effect and irrationality of repair. The establishment of structural health monitoring system, strengthening of biological control and promotion of basic research on mechanical performance of timber structures are the important foundations and methods for the protection and repair of ancient buildings.