A strong earthquake commonly triggers the occurrence of multiple aftershocks. Three structures with different layers and crosses and an ordinary flat frame structure were designed with reference to the current codes of China. Based on the incremental dynamic analysis method, the Park-Ang damage index was adopted as the parameter of structural response, and the peak ground acceleration was used as the parameter of the ground motion intensity. Then, the vulnerability curves of the step-terrace structures and the ordinary flat frame structure under a mainshock and aftershocks were obtained. The vulnerabilities of the step-terrace structure and the ordinary flat frame structure were compared and analyzed, and the influence of aftershocks on the vulnerability of each structure was studied. The anti-collapse abilities of the structures were evaluated based on the collapse margin ratio (CMR), and the safety reserves of the structures were compared. The results show that the aftershocks increased the exceedance probability of the structure, and with the increase of the aftershock intensity, the exceedance probability was bigger. Compared with the ground structure, the exceedance probability of the step-terrace structure was higher, and the influence of the number of layers and the number of falling spans on the vulnerability of the structure was significant. Compared with the ordinary flat frame structure, the anti-collapse reserve coefficient of the step-terrace structure was small, and the anti-collapse safety reserve was lower. For the step-terrace structure, the increase in the number of layers will reduce the collapse of the security reserves, and the number of layers has a great impact on the CMR.