The terminal No. II of Shanghai Pudong International Airport is located at Pudong District of Shanghai City near shore of East China Sea, and the area of the long-span terminal is 400 m × 200 m. The construction site of the terminal locates on the irregular topography, and its alluvium achieves about 300 m in thickness. The spatial correlation of seismic ground motion, as well as the amplification of soft alluvium and the effect of irregular topography, should be considered. This paper uses a simplified method to obtain the response spectrum of the engineering bedrock under the irregular topography. The spectrum is used to generate the sets of spatially correlative horizontal and vertical seismic motions. The surface ground motion was calculated under incidence of the spatially correlative seismic motion by 2D finite element method (FEM) model considering nonlinear properties of the soil by means of the equivalent linear method. In order to compare the effect of 2D irregular topography, the seismic response analysis of 1D model is carried out by using the equivalent linear method. For indicating the effect of the spatial correlation of input motions, the horizontal uniform inputs, as well as the horizontal and vertical uniform input are carried out for the seismic response analysis of the site. Finally, some characteristics of seismic ground motion calculated for previously mentioned cases are compared.