In order to investigate the dynamic responses and damage distribution of low layers of masonry structures in village buildings during strong earthquakes, finite element models of masonry structures are established on the ABAQUS software program based on the survey and the material test of rural buildings; the analysis considered the different details of seismic design. The vibration characteristics, displacement response, and the damage configuration of each model are then compared based on the results of dynamic characteristic analysis and elastic-plastic time-history analysis. Research results show that the vibration regularity and model are not changed by the reasonable setting details of seismic design in low layers of masonry structures. Nevertheless, the structural column is involved in the anti-lateral work to some extent, such that the basic period of the structure is slightly decreased. The dynamic displacement responses of structures are efficiently restricted by the column in the elastic period, and the energy dissipation capacity of masonry structures can be improved in the plastic period. However, the imbalance between longitudinal and lateral stiffness could be exacerbated once the structure stiffness is degraded. When a structure comes up against a major earthquake, the seismic performance can be improved effectively by the structural column and ring beam; for example, the development of cracks in the bearing cross-wall can be inhibited, and the roof damage can suppress the bearing failure, thereby weakening the torsion effect.