There are many limitations for important hydraulic project’s rock site at present, such as envelopment effects of probability-consistent response spectrum, and frequency stationarity in acceleration time history, etc.. In order to overcome those shortcomings, a new method of determination of ground motion input parameters for important hydraulic project’s rock site has been put forward in this study. The effective peak acceleration with different exceeding probability, as well as the dominant potential seismic source which had the largest contribution to the site, have been determined by using probabilistic seismic hazard analysis, which based on effective peak acceleration. The magnitude of scenario earthquake within the dominant potential earthquake sources is determined by the largest probability of magnitude-spatial joint distribution,and the corresponding design response spectra is determined by the attenuation relationship of acceleration response spectra. Then evolutionary power spectrum is gained according to scenario earthquake and the attenuation relationships of evolutionary power spectrum model parameters, and the amplitude and frequency non-stationary acceleration time history at dam site are synthesized by using trigonometric series superposition method, which based on evolutionary power spectra and minimum phase spectrum. In a case study of Shapai dam site, based on the evaluation of regional seismic activities and seismotectonic environment, ground motion input parameters at dam rock site with different exceeding probability, including the effective peak acceleration, design response spectra, amplitude and frequency non-stationarity acceleration time history, are determined.