Abstract: In order to study the seismic performance of bottom-frame masonry structures under complex three-dimensional vibration characteristics, six types of ground shaking records with complex characteristics were selected from the ground shaking database of the Pacific Earthquake Engineering Research Center (PEERC) and inputted into the numerical models of bottom-frame masonry structures and their seismic isolation structures with two different storeys, and the seismic response parameters were calculated under the dynamical-elastic-plastic time course to evaluate their seismic performance under complex ground shaking. The results show that the impulse-type earthquake can cause more intense seismic response for the base frame masonry structure, and the soft soil impulse-type earthquake can cause more seismic response for the base frame masonry isolation structure. Analyzed from the point of view of velocity impulse effect, velocity impulse effect reduces the damping rate of base frame masonry isolation structures at all storeys. Foundation isolation has a certain effect on improving the seismic performance of the bottom frame masonry structure, considering the seismic performance and economic rationality, the foundation isolation design is not recommended for the low bottom frame masonry structure, while for the higher bottom frame masonry structure, the foundation isolation can effectively reduce the tensile damage of the brick masonry on the upper part of the structure.