The analysis on earthquake response of one multi-tower isolation structure with an enlarged base in rare earthquake and aftershocks was carried out using elastic time history analysis method. It includes the damping effect of structure, plastic deformation of members and plastic hinges distribution in structure. The results show that isolation structure comes to plastic state under rare earthquake lighter, vertical elements remain flexible under earthquake aftershocks, the plastic hinges on horizontal members are deepen, but the structure can meet the requirement while it is renovated. Plastic hinges first appear in the bottom of structure, then they gradually develop upwards, Plastic hinges are generated at the ends of beams, but not occur in columns and walls. The displacement of structure under rare earthquake is mainly concentrated on isolation layer and it can take energy consumption by large displacement.