Mid-story isolation eccentric structures with tower–podium are examples of vertically irregular structures. Its seismic performance and the related mechanisms, however, have not been experimentally examined. In this study, a representative model of a practical mid-story isolation eccentric structure with a large podium was fabricated, tested, and simulated to investigate its seismic response under different earthquakes. The results were then compared to those of an anti-seismic model without the isolation layer. The results show that (a) the mid-story isolation eccentric structure with tower–podium has the similar characteristics of seismic performance with the regular story isolation structure; (b) as the peak acceleration value increases, the podium could quickly enter the elastoplastic state and reach the medium damage level. The damage extent in the second layer of the podium is larger than that in its first layer. It is thus recommended that the structural components of the podium be strengthened, and the elastoplastic displacement angle limit of the podium be increased. The modeling results also indicate the torsional effects of such eccentric structure are effectively inhibited. Our study enhances the understanding of the mid-story isolation eccentric structure with tower–podium and pioneers a guide to the seismic design of such a structure.