An one-dimensional soil layer model is employed to analyze the site effects of the designing ground motion in five kinds of non-hard rock sites, including firm rock site, soft rock site, upper bound soft-to-medium soil site, soft-to-medium soil site and soft soil site, for designing the foundation of AP1000 nuclear island (NI) structure. In this study, the shear wave velocity in the bedrock of the computational model is selected as 700, 1 100 or 2 438 m/s. The input motion of the bedrock is taken as RG1.60, AP1000 and HAD101 spectra (with 5 damping ratios) matching with the synthetic acceleration time histories of ground motion provided in the relative technical documents and standards, respectively. Analytical results indicate that non-hard rock sites induce the significant changes of the peak ground acceleration and response spectrum of the ground motion, which is enhanced further by a softer site. The effects of non-hard rock sites, except the soft sites, amplify the peak ground acceleration and response spectrum. However, the effect of the soft site increases the peak ground acceleration and response spectrum in a lower frequency range, and it is opposite in a higher frequency range. The peak ground acceleration and response spectrum of the site ground motion are significantly influenced by the changes of the bedrock and its shear wave velocity of all non-hard rock sites. Moreover, the effect is proportional to the shear wave velocity of the bedrock, and the ground motion decreases obviously with the increase of shear wave velocity. The ground motion is unaffected by the shear wave velocity as the site changes from hard to soft. Considering the great effects of the site type and the bedrock selection on ground motion, it is thus necessary to analyze the applicability of the sites by using the AP1000 standard design in the nuclear power plant construction in China.