Seismic behavior of bedrock foundation remains as one of the most fundamental and important problems concerning the stability and safety of nuclear power plants. The dynamic FEM (Finite Element Method) is commonly utilized in analyzing the seismic responses of bedrock; while in recent decades, the DEM (Distinct Element Method) has attracted more and more attentions, which has a better capability of simulating the sliding and separation of discontinuities in dynamic simulations. In this study, the FEM and DEM were adopted to investigate the seismic behavior of the bedrock of a nuclear power plant located in Japan, and the differences between the two methods in dynamic simulations were illuminated. Simulation results using FEM and DEM models without discontinuities agree well with each other, exhibiting an amplification effect of intact bedrock on the seismic wave propagation. Numerical simulation results obtained from the models containing faults give similar responses of bedrock to the input seismic waves; however, the FEM model underestimates the weakening effect of discontinuities on the propagation of seismic waves due to that it cannot represent well the large deformational behavior of discontinuities. When large deformation happens due to large seismic loads, the DEM can be regarded as a better method in seismic response evaluations of bedrock with discontinuities.