The reasonable assessment of potential damage type of masonry structures in seismic-prone zone is very significant to strengthen existing masonry structures and guide the construction of the new building. The primary objective of the study is to propose and determine a reasonable assessment index to predict the damage type of masonry structures in different seismic intensity zones using the survey results of the 2008 Wenchuan earthquake and variance analyses comparison methods. Three potential theory assessment indexes are considered in the evaluation of damage of masonry structures, including wall density index Iw, strength index Isq, and combined index Isd. In order to compare the feasibility of the three indexes, One-way analysis of variance and Scheffé’s method were used for in-depth discussion. Based on the proposed assessment indexes, further analyses and recommendations were provided. Results show the combined index Isd has a high potential to predict the damage levels of masonry structures. Based on the study, several recommendations were provided for the masonry structures in seismic-prone zones.