This paper analyses the seismic damage of 3 991 masonry structures in Dujiangyan during Wenchuan earthquake, to understand the seismic damage characteristics and seismic capacity of masonry structures in different intensity regions. Firstly, seismic damage of Dujiangyan masonry structure is observed. The results display that the location of this kind of structure system is easy to be damaged: vertical and horizontal walls, openings, joints of vertical and horizontal walls, window (lower) walls and tie columns; However, a large number of masonry structures are basically intact after seismic design. Using the method of numerical statistical analysis to analyze the survey data, the relationship between the sample and the seismic damage grade and the vulnerability matrix are given, and the nonlinear model of the seismic damage grade and vulnerability under different intensity grades in the multi intensity region is established. Considering the seismic damage of the structure under the influence of seismic fortification factors, the general law of seismic damage index and intensity of the structure in multiintensity region is analyzed by regression curve. The results can be used for reference in the revision of intensity scale and vulnerability analysis.