The new staggered story isolated structure is developed according to the base-isolated structure and the mid-story isolated structure. Quantitative calculation and evaluation of seismic damage are very important for structural safety. In this paper, the seismic damage evaluation of a new staggered story isolated structure is studied by numerical simulation and damage index calculation. A new staggered story isolated structure is established, and the effects of different layers and different chassis areas on the seismic response of the structure are studied. When the position of the bottom isolated layer stays the same, the upper isolated layer is set at different layers, which is set to the top of the 3rd, 6th and 9th layers. When the upper isolated layer keeps at the top of the 3rd layer, the chassis area is set at a different area, which is 26 m × 26 m, 36 m × 36 m and 46 m × 46 m. The results show that the new staggered story isolated structure has good isolated effects under the ground motion. For the structure set upper isolation layer is lower, the inter-layer shear force, inter-layer acceleration and inter-layer displacement are reduced. The energy dissipation effect of the structure improves. The core tube is less damaged and the plastic hinge is smaller. With the increase of chassis area, the isolated effect of the part above the upper isolated layer is good, while the shear force and acceleration of the part below the upper isolated layer of the structure increase, the damage at the core tube changed little and the appearance of the plastic hinge increased. Under earthquakes, with the change in position of the upper isolated layer and the area of the chassis of the new staggered story isolated structure, the displacement, tensile stress and compressive stress of the isolated bearing still meet the requirements of the standard.