ANSYS has become an effective tool for finite element analysis of masonry structure, but there is few common conclusions for reference. According to the characteristics of ANSYS and the essence of the analysis, some key problems in finite element analysis of masonry structure with ANSYS, such as structural modelling, material constitution, the damage criterion, iterative algorithm, convergence criterion, simulation of prestressing force and so on, are discussed in this paper. Based on the test results of typical masonry structures, the applicability of ANSYS to masonry structural analysis is studied and some suggestions for the application of ANSYS are presented.