Superstructures of seismically isolated structure keep in elastic or slightly elastic-plastic range subjected to rare earthquakes, thereby protecting superstructure effectively. However, very-rare earthquakes may happen in design reference period due to uncertainty of earthquake intensity and character. On basis of “survive rare earthquakes by sustaining significant damage but without globally collapsing” design, horizontal deformation of isolation bearings and overturning resistance under very-rare earthquakes, performance and cost of seismically isolated structure based on “survive very-rare earthquakes” are worth researching. Dynamic responses of three seismically isolated structures with different heights are obtained from elastic-plastic time history analysis. Main failure modes of seismically isolated structures subjected to very-rare earthquakes are presented by comparing the responses such as inter-story drift ratios, horizontal displacements of isolation bearings and overturning moments. The results show that under very-rare earthquakes, horizontal displacements of isolation bearing in all three classic seismically isolated structures are excessive, while other two responses both meet the requirements. With isolation bearings increasing suitably, new structures can avoid destruction by deformation of isolation layer increasing and survive very-rare earthquakes, while isolation effectiveness reduce slightly. Reducing the aspect ratio of superstructure appropriately can control the overturning of whole structure especially high-rise structure subjected to very- rare earthquakes. Therefore, considering both safety and economy, it is an effective and economical way to increase the ultimate displacement of isolation bearing, appropriately reduce the aspect ratio of high-rise seismically isolated structures, and realize resistance ability of isolated buildings subjected to very-rare earthquake.