On the basis of analyzing the special requirements for security for the high-level radioactive waste storage structure, the seismic design parameters of this engineering are determined. There is no criterion that determines the design ground motion parameters of underground engineering. Based on the thought of the severest design ground motion, the basic methods and principles to determine the design ground motion parameters of underground structure are put forward. The characteristics of high-level radioactive waste storage structure are analyzed, and the frequencies corresponding to the maxim modal participation factors are gain. Combined with the analysis of the site geological safety assessment report, through the initial search and optimization with the method of numerical simulation, the design ground motion parameters of the high-level radioactive waste storage structure on the specific site is determined. The method is easy to operate, which can also be applied in other important deep underground engineerings.