The site seismic response analysis is the most important work in the safety evaluation of nuclear power plant. The proposed Sichuan nuclear power plant is in sedimentary rock strata. The common feature of sedimentary rock strata is the nonuniformity of rock. The strata are characterized by the possesses a different angles, different physical and mechanical characteristics, different weathering degrees, and different lithofacies. These features listed above make the site seismic response analysis more difficult. In order to accurately estimate the strata condition’s influence to the seismic response, the authors studied the following issues: how the rigidity degree of the strata influence to seismic acceleration amplification characteristics, how the weathering degree of sedimentary rock strata influence to seismic waves amplification characteristics, how “Basin effect” influence seismic waves amplification characteristics, the random characteristics of seismic waves of its own, how to design the model on the site seismic response analysis and engineering analysis software in sedimentary rock strata.