In this paper,a dynamic analysis for pumping station structure of NPP is carried out using Super SAP and CLASSI program under the condition of ultimate safety ground motion and operation safety ground motion.The series of seismic response were transformed by FFT(Fast Fourier Transform) after the time-history analysis and in turn the Floor Response Spectra(FRS) of structure is achieved.The calculation results under the two conditions are compared in detail.Based on the comparison made between the two results(considering SSI and fixed base) under-mentionedi,t indicates that this method and program is practical.It also clearly shows there are significant effects of SSI on the FRS peak value,FRS shape and the response spectrum value in the high frequency domain.