In recent years, there has been serious damage to embankments on liquefied ground because of large earthquakes. To understand such damage, many two-dimensional shaking table model tests have been performed, in both gravitational and centrifugal fields, to investigate the dynamic behavior and residual displacement of embankments and river dikes on liquefiable ground. In recent years, three-dimensional numerical analysis has been used in practical design because it is difficult to consider the complex dynamic behaviors of three-dimensional embankments and the surrounding liquefied ground in a two-dimensional analysis. However, there are only a limited number of cases in which the applicability of three-dimensional analysis has been validated based on comparisons with true values derived from model tests or data from actual disasters. Therefore, in this study, a series of shaking table tests were conducted to investigate the seismic behavior of a three-dimensional embankment on liquefiable ground. In addition, the effect of the shaking direction on the seismic behavior of the embankment was evaluated. The experiment revealed that the residual deformation and its dominant direction were significantly affected by the three-dimensional shape and total weight of the embankment, not by the shaking direction. This result indicates that the influence of the three-dimensional shape of the embankment on the deformation behavior cannot be ignored, and that the influence should be properly evaluated in seismic design.