To research the dynamic characteristics and vibration mechanism of low-story masonry structures in rural buildings, we used ABAQUS to establish seven finite element models based on a survey of rural buildings. In the models, we considered structure layout, strength of the materials, and mesh density. Then, we analyzed the dynamic characteristics of each model and compared their vibration shapes, modal components, and vibration periods. The results show that the vibration characteristics of traditional masonry structures are not conducive to seismic design and that the degradation of materials reduces the bearing capacity of the structures, while at the same time amplifying the seismic action of the wall oscillation component, which increases the probability of outward collapse in earthquake. If the basic vibration type is horizontal along the transverse direction, the seismic capacity of the structure is improved with respect to both the bearing and deformation abilities of load-bearing walls. In addition, we propose ABAQUS mesh requirements for shell elements with respect to thickness.