Many metropolises, such as Tokyo, Osaka, and Nagoya, are on the sedimentary basin in Japan. On the sedimentary basin, the characteristics of seismic ground motion varies with the incidence directions of seismic waves due to the complicated soil structure. Especially, the predominant period of the seismic ground motion, which is very important in the design of high-rise buildings, often varies with the direction of the hypocenter. In this study, we develop a new method to evaluate the dynamic characteristics of the sedimentary basin using the three dimensional finite difference method and the reciprocity theorem of Green's function. The finite difference method is advantageous to the complicated soil structure. In addition, the calculation cost is dramatically reduced using the reciprocity theorem of Green's function. By using our new method, the fluctuation range of the predominant period of the seismic ground motion can be revealed for the observation point on the sedimentary basin.