Abstract: Based on finite element theory, the base-isolated and fixed solid models of masonry structure with concrete frame at lower two stories were established by SAP2000 Nonlinear software. Then, seismic response analysis under the real prerecorded earthquake excitation in three directions (two horizontal and one vertical) was investigated by nonlinear time history analysis method. The results show that the horizontal seismic responses of the base-isolated masonry structure with concrete frames at lower two stories are remarkably less than those of the non-isolated structure, especially in the transition story with abrupt change of stiffness. However, the vertical seismic responses of the base-isolated structure may increase, which will endanger the security of the base-isolated structure.