In order to verify the reliability of numerical site response analysis program, both soil free-field and base rock input motions should be provided. Beside the field earthquake motion records, the most effective testing method for obtaining the above motions is the dynamic geotechnical centrifuge test. However, need is to verify if the motion recorded at the base of the soil model container in the centrifuge facility is the true base rock input motion or not. In this paper, the appropriate input motion measurement method for the verification of seismic response analysis is examined by dynamic geotechnical centrifuge test and using three-dimensional finite difference analysis results. From the results, it appears that the ESB (equivalent shear beam) model container distorts downward the propagating wave with larger magnitude of centrifugal acceleration and base rock input motion. Thus, the distortion makes the measurement of the base rock outcrop motion difficult which is essential for extracting the base rock incident motion. However, the base rock outcrop motion generated by using deconvolution method is free from the distortion effect of centrifugal acceleration.